Starting phenix.real_space_refine on Wed Mar 5 19:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.map" model { file = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2025/7won_32652.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2098 2.51 5 N 556 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.87, per 1000 atoms: 2.07 Number of scatterers: 3318 At special positions: 0 Unit cell: (73.132, 84.024, 80.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 649 8.00 N 556 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 372.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 8 sheets defined 1.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.532A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.501A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 51 removed outlier: 5.896A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.748A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.113A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104 66 hydrogen bonds defined for protein. 168 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: 0.80 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 538 1.30 - 1.43: 1004 1.43 - 1.56: 1840 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 3401 Sorted by residual: bond pdb=" C ARG H 106 " pdb=" N SER H 107 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.98e+01 bond pdb=" CA ARG H 106 " pdb=" C ARG H 106 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" CA ARG H 106 " pdb=" CB ARG H 106 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.58e-02 4.01e+03 1.27e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 4523 2.84 - 5.69: 80 5.69 - 8.53: 12 8.53 - 11.37: 2 11.37 - 14.22: 3 Bond angle restraints: 4620 Sorted by residual: angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 109.52 121.19 -11.67 1.55e+00 4.16e-01 5.67e+01 angle pdb=" O VAL H 100 " pdb=" C VAL H 100 " pdb=" N GLN H 101 " ideal model delta sigma weight residual 122.57 114.38 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.35 101.53 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" C ARG H 106 " pdb=" N SER H 107 " pdb=" CA SER H 107 " ideal model delta sigma weight residual 121.54 109.28 12.26 1.91e+00 2.74e-01 4.12e+01 angle pdb=" CA ARG H 106 " pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 120.70 127.27 -6.57 1.03e+00 9.43e-01 4.06e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 1823 20.55 - 41.09: 143 41.09 - 61.64: 19 61.64 - 82.18: 6 82.18 - 102.73: 10 Dihedral angle restraints: 2001 sinusoidal: 787 harmonic: 1214 Sorted by residual: dihedral pdb=" CA PHE F 429 " pdb=" C PHE F 429 " pdb=" N THR F 430 " pdb=" CA THR F 430 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 365 0.059 - 0.119: 101 0.119 - 0.178: 19 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 489 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 100 " 0.042 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" C VAL H 100 " -0.138 2.00e-02 2.50e+03 pdb=" O VAL H 100 " 0.051 2.00e-02 2.50e+03 pdb=" N GLN H 101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO F 463 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 56 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 57 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 50 2.61 - 3.18: 2613 3.18 - 3.75: 4748 3.75 - 4.33: 6402 4.33 - 4.90: 10870 Nonbonded interactions: 24683 Sorted by model distance: nonbonded pdb=" O ARG H 106 " pdb=" C SER H 107 " model vdw 2.035 3.270 nonbonded pdb=" O SER F 371 " pdb=" NH1 ARG H 106 " model vdw 2.238 3.120 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.276 3.040 nonbonded pdb=" O ARG H 106 " pdb=" CA SER H 107 " model vdw 2.278 2.776 nonbonded pdb=" OG SER F 349 " pdb=" O LEU F 452 " model vdw 2.302 3.040 ... (remaining 24678 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.460 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 3401 Z= 0.385 Angle : 0.977 14.217 4620 Z= 0.564 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 16.809 102.726 1232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.35), residues: 419 helix: -4.82 (0.44), residues: 14 sheet: -2.40 (0.44), residues: 127 loop : -3.30 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 436 HIS 0.006 0.003 HIS H 35 PHE 0.011 0.002 PHE F 400 TYR 0.021 0.002 TYR H 104 ARG 0.007 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8755 (p0) cc_final: 0.8457 (p0) REVERT: F 474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5872 (tm-30) REVERT: L 16 GLN cc_start: 0.8730 (mm110) cc_final: 0.8170 (mp10) REVERT: H 16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1977 (mmt180) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1817 time to fit residues: 20.3300 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 106 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 370 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 487 ASN L 6 GLN L 16 GLN L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109778 restraints weight = 5056.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111950 restraints weight = 3623.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113400 restraints weight = 2905.026| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3401 Z= 0.330 Angle : 0.696 8.421 4620 Z= 0.354 Chirality : 0.048 0.214 492 Planarity : 0.005 0.045 600 Dihedral : 12.083 78.853 522 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 4.79 % Allowed : 19.72 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.38), residues: 419 helix: -4.52 (0.76), residues: 14 sheet: -2.34 (0.44), residues: 132 loop : -2.88 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE F 338 TYR 0.017 0.002 TYR F 495 ARG 0.004 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.342 Fit side-chains REVERT: F 346 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.7093 (tpp80) REVERT: F 354 ASN cc_start: 0.8886 (p0) cc_final: 0.8562 (p0) REVERT: F 427 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7962 (t0) REVERT: F 474 GLN cc_start: 0.6092 (tp40) cc_final: 0.5767 (tm-30) REVERT: L 6 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: L 16 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8098 (mp10) REVERT: H 16 ARG cc_start: 0.2304 (mmt180) cc_final: 0.1996 (mmt180) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.1879 time to fit residues: 21.6226 Evaluate side-chains 92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN L 6 GLN L 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115294 restraints weight = 4928.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118044 restraints weight = 3290.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119994 restraints weight = 2498.342| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3401 Z= 0.222 Angle : 0.655 9.737 4620 Z= 0.324 Chirality : 0.046 0.244 492 Planarity : 0.004 0.038 600 Dihedral : 10.322 66.025 518 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.38 % Allowed : 20.85 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.39), residues: 419 helix: -4.60 (0.68), residues: 14 sheet: -2.04 (0.45), residues: 133 loop : -2.60 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE F 338 TYR 0.014 0.001 TYR F 369 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8860 (p0) cc_final: 0.8500 (p0) REVERT: F 474 GLN cc_start: 0.5912 (tp40) cc_final: 0.5372 (tm-30) REVERT: L 16 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8121 (mp10) REVERT: H 16 ARG cc_start: 0.2433 (mmt180) cc_final: 0.0200 (mmt180) REVERT: H 113 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8495 (m-30) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.2116 time to fit residues: 22.1079 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113500 restraints weight = 5072.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116246 restraints weight = 3373.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118212 restraints weight = 2558.294| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3401 Z= 0.267 Angle : 0.662 9.800 4620 Z= 0.325 Chirality : 0.047 0.232 492 Planarity : 0.004 0.033 600 Dihedral : 9.134 56.126 518 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.79 % Allowed : 19.44 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.40), residues: 419 helix: -4.55 (0.71), residues: 14 sheet: -1.96 (0.46), residues: 133 loop : -2.52 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.013 0.002 PHE F 338 TYR 0.023 0.002 TYR H 114 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.367 Fit side-chains REVERT: F 354 ASN cc_start: 0.8898 (p0) cc_final: 0.8574 (p0) REVERT: F 474 GLN cc_start: 0.5973 (tp40) cc_final: 0.5341 (tm-30) REVERT: L 16 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8128 (mp10) REVERT: H 16 ARG cc_start: 0.2216 (mmt180) cc_final: 0.1872 (mmt180) REVERT: H 113 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8453 (m-30) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.1788 time to fit residues: 19.3055 Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111238 restraints weight = 5021.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113962 restraints weight = 3404.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115778 restraints weight = 2616.035| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3401 Z= 0.248 Angle : 0.662 9.703 4620 Z= 0.325 Chirality : 0.047 0.212 492 Planarity : 0.004 0.034 600 Dihedral : 8.396 56.738 518 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.35 % Allowed : 20.00 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.40), residues: 419 helix: -4.61 (0.69), residues: 14 sheet: -1.88 (0.47), residues: 127 loop : -2.41 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.013 0.002 PHE F 347 TYR 0.030 0.002 TYR H 114 ARG 0.006 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.377 Fit side-chains REVERT: F 354 ASN cc_start: 0.8880 (p0) cc_final: 0.8532 (p0) REVERT: F 474 GLN cc_start: 0.5980 (tp40) cc_final: 0.5379 (tm-30) REVERT: L 16 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8150 (mp10) REVERT: H 16 ARG cc_start: 0.2354 (mmt180) cc_final: 0.1976 (mmt180) REVERT: H 53 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7091 (t80) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.1801 time to fit residues: 19.9681 Evaluate side-chains 93 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.133270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111305 restraints weight = 5110.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113987 restraints weight = 3369.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115965 restraints weight = 2554.945| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3401 Z= 0.255 Angle : 0.667 9.981 4620 Z= 0.328 Chirality : 0.047 0.222 492 Planarity : 0.004 0.033 600 Dihedral : 8.063 58.631 518 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.79 % Allowed : 21.41 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.40), residues: 419 helix: -4.71 (0.59), residues: 14 sheet: -1.83 (0.47), residues: 127 loop : -2.38 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.002 PHE F 338 TYR 0.029 0.002 TYR H 114 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.367 Fit side-chains REVERT: F 354 ASN cc_start: 0.8884 (p0) cc_final: 0.8530 (p0) REVERT: F 427 ASP cc_start: 0.8321 (t0) cc_final: 0.8109 (t0) REVERT: F 474 GLN cc_start: 0.6022 (tp40) cc_final: 0.5346 (tm-30) REVERT: L 16 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8123 (mp10) REVERT: H 16 ARG cc_start: 0.2220 (mmt180) cc_final: 0.1826 (mmt180) REVERT: H 53 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7323 (t80) REVERT: H 113 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8400 (m-30) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1879 time to fit residues: 19.5800 Evaluate side-chains 92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 23 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.131976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111239 restraints weight = 4984.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113388 restraints weight = 3559.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115066 restraints weight = 2831.358| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3401 Z= 0.244 Angle : 0.659 10.065 4620 Z= 0.324 Chirality : 0.046 0.230 492 Planarity : 0.004 0.032 600 Dihedral : 7.724 59.447 518 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 5.07 % Allowed : 21.97 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.40), residues: 419 helix: -4.91 (0.40), residues: 20 sheet: -1.77 (0.48), residues: 127 loop : -2.25 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.002 PHE F 429 TYR 0.027 0.002 TYR H 114 ARG 0.005 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.357 Fit side-chains REVERT: F 354 ASN cc_start: 0.8868 (p0) cc_final: 0.8522 (p0) REVERT: F 474 GLN cc_start: 0.5969 (tp40) cc_final: 0.5335 (tm-30) REVERT: L 16 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8092 (mp10) REVERT: H 16 ARG cc_start: 0.2429 (mmt180) cc_final: 0.2023 (mmt180) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.1753 time to fit residues: 18.3212 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117572 restraints weight = 4905.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120391 restraints weight = 3220.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122361 restraints weight = 2434.973| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3401 Z= 0.164 Angle : 0.640 10.011 4620 Z= 0.306 Chirality : 0.045 0.240 492 Planarity : 0.004 0.033 600 Dihedral : 7.003 55.638 518 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.38 % Allowed : 23.66 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.40), residues: 419 helix: -4.87 (0.45), residues: 20 sheet: -1.44 (0.49), residues: 126 loop : -2.12 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 100 HIS 0.005 0.002 HIS H 35 PHE 0.008 0.001 PHE F 456 TYR 0.018 0.001 TYR H 114 ARG 0.004 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.382 Fit side-chains REVERT: F 354 ASN cc_start: 0.8803 (p0) cc_final: 0.8451 (p0) REVERT: F 474 GLN cc_start: 0.5898 (tp40) cc_final: 0.5354 (tm-30) REVERT: L 16 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8076 (mp10) REVERT: L 93 TYR cc_start: 0.8239 (t80) cc_final: 0.7995 (t80) REVERT: H 16 ARG cc_start: 0.2541 (mmt180) cc_final: -0.0516 (mpt180) REVERT: H 25 SER cc_start: 0.9328 (t) cc_final: 0.9021 (m) outliers start: 12 outliers final: 10 residues processed: 87 average time/residue: 0.1836 time to fit residues: 19.0319 Evaluate side-chains 86 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.134226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112199 restraints weight = 4972.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115026 restraints weight = 3296.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116919 restraints weight = 2491.637| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3401 Z= 0.263 Angle : 0.675 9.851 4620 Z= 0.327 Chirality : 0.046 0.243 492 Planarity : 0.004 0.031 600 Dihedral : 7.003 53.438 518 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.38 % Allowed : 24.23 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.40), residues: 419 helix: -4.75 (0.47), residues: 20 sheet: -1.50 (0.49), residues: 125 loop : -2.11 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE F 338 TYR 0.015 0.002 TYR H 114 ARG 0.004 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.338 Fit side-chains REVERT: F 354 ASN cc_start: 0.8845 (p0) cc_final: 0.8494 (p0) REVERT: F 474 GLN cc_start: 0.5882 (tp40) cc_final: 0.5337 (tm-30) REVERT: L 16 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8096 (mp10) REVERT: L 93 TYR cc_start: 0.8236 (t80) cc_final: 0.7996 (t80) REVERT: H 16 ARG cc_start: 0.2373 (mmt180) cc_final: 0.1963 (mmt180) outliers start: 12 outliers final: 11 residues processed: 85 average time/residue: 0.1796 time to fit residues: 18.0501 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111620 restraints weight = 4977.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114263 restraints weight = 3328.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116211 restraints weight = 2555.379| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3401 Z= 0.284 Angle : 0.687 10.187 4620 Z= 0.334 Chirality : 0.047 0.240 492 Planarity : 0.004 0.032 600 Dihedral : 7.146 54.226 518 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.66 % Allowed : 24.51 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.41), residues: 419 helix: -4.92 (0.62), residues: 14 sheet: -1.49 (0.49), residues: 126 loop : -2.07 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.002 PHE F 338 TYR 0.014 0.002 TYR L 93 ARG 0.004 0.001 ARG F 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.356 Fit side-chains REVERT: F 354 ASN cc_start: 0.8850 (p0) cc_final: 0.8481 (p0) REVERT: F 474 GLN cc_start: 0.6043 (tp40) cc_final: 0.5357 (tm-30) REVERT: L 16 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8109 (mp10) REVERT: L 93 TYR cc_start: 0.8239 (t80) cc_final: 0.7959 (t80) REVERT: H 16 ARG cc_start: 0.2286 (mmt180) cc_final: 0.1879 (mmt180) outliers start: 13 outliers final: 12 residues processed: 88 average time/residue: 0.1826 time to fit residues: 19.0769 Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110937 restraints weight = 5068.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113597 restraints weight = 3378.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115577 restraints weight = 2584.777| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3401 Z= 0.319 Angle : 0.710 10.926 4620 Z= 0.346 Chirality : 0.047 0.241 492 Planarity : 0.004 0.032 600 Dihedral : 7.356 55.638 518 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.66 % Allowed : 25.07 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.41), residues: 419 helix: -4.91 (0.64), residues: 14 sheet: -1.51 (0.49), residues: 126 loop : -2.02 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.007 0.002 HIS H 35 PHE 0.015 0.002 PHE F 338 TYR 0.013 0.002 TYR L 93 ARG 0.004 0.001 ARG F 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.40 seconds wall clock time: 34 minutes 51.90 seconds (2091.90 seconds total)