Starting phenix.real_space_refine on Sun Apr 27 16:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4b_45180/04_2025/9c4b_45180.cif" } resolution = 3.4 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= 0.042 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 24 5.16 5 C 1950 2.51 5 N 525 2.21 5 O 581 1.98 5 H 3030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6110 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 2 Time building chain proxies: 4.40, per 1000 atoms: 0.72 Number of scatterers: 6110 At special positions: 0 Unit cell: (81.9, 69.3, 78.75, 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 24 16.00 O 581 8.00 N 525 7.00 C 1950 6.00 H 3030 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.71 Conformation dependent library (CDL) restraints added in 451.2 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 44.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.902A pdb=" N ALA A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.578A pdb=" N ILE A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.683A pdb=" N SER A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.536A pdb=" N CYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.642A pdb=" N LEU A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.627A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 422 through 428 removed outlier: 4.025A pdb=" N ARG A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.428A pdb=" N ILE A 18 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.574A pdb=" N VAL A 193 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 5.817A pdb=" N LEU A 168 " --> pdb=" O ILE A 349 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 357 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: 2.69 Time building geometry restraints manager: 2.10 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: 3021 1.03 - 1.23: 13 1.23 - 1.42: 1310 1.42 - 1.62: 1797 1.62 - 1.81: 39 Bond restraints: 6180 Sorted by residual: bond pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N GLN A 281 " pdb=" CA GLN A 281 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.23e+01 bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.33e-02 5.65e+03 8.32e+00 bond pdb=" N GLU A 208 " pdb=" H GLU A 208 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 6175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11102 2.85 - 5.70: 52 5.70 - 8.56: 3 8.56 - 11.41: 1 11.41 - 14.26: 1 Bond angle restraints: 11159 Sorted by residual: angle pdb=" N GLN A 211 " pdb=" CA GLN A 211 " pdb=" C GLN A 211 " ideal model delta sigma weight residual 112.89 98.63 14.26 1.24e+00 6.50e-01 1.32e+02 angle pdb=" N ALA A 279 " pdb=" CA ALA A 279 " pdb=" C ALA A 279 " ideal model delta sigma weight residual 112.90 105.10 7.80 1.31e+00 5.83e-01 3.54e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 113.30 105.83 7.47 1.34e+00 5.57e-01 3.11e+01 angle pdb=" C PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta sigma weight residual 110.17 119.40 -9.23 1.69e+00 3.50e-01 2.98e+01 angle pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " pdb=" CG PHE A 210 " ideal model delta sigma weight residual 113.80 108.84 4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 11154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2546 17.69 - 35.39: 255 35.39 - 53.08: 89 53.08 - 70.77: 33 70.77 - 88.47: 9 Dihedral angle restraints: 2932 sinusoidal: 1599 harmonic: 1333 Sorted by residual: dihedral pdb=" C PHE A 210 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA LYS A 240 " pdb=" C LYS A 240 " pdb=" N GLU A 241 " pdb=" CA GLU A 241 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 223 " pdb=" C ILE A 223 " pdb=" N ALA A 224 " pdb=" CA ALA A 224 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 340 0.042 - 0.083: 86 0.083 - 0.125: 40 0.125 - 0.167: 4 0.167 - 0.209: 2 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA PHE A 210 " pdb=" N PHE A 210 " pdb=" C PHE A 210 " pdb=" CB PHE A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 92 " pdb=" N MET A 92 " pdb=" C MET A 92 " pdb=" CB MET A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA MET A 254 " pdb=" N MET A 254 " pdb=" C MET A 254 " pdb=" CB MET A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 469 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 211 " -0.254 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CD GLN A 211 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 211 " 0.241 2.00e-02 2.50e+03 pdb=" NE2 GLN A 211 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN A 211 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN A 211 " -0.510 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 281 " 0.141 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CD GLN A 281 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 281 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN A 281 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 281 " -0.226 2.00e-02 2.50e+03 pdb="HE22 GLN A 281 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 210 " 0.059 2.00e-02 2.50e+03 2.66e-02 2.12e+01 pdb=" CG PHE A 210 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 210 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 210 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 210 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 210 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 210 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 210 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 210 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 210 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 210 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 210 " 0.011 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 452 2.19 - 2.80: 12514 2.80 - 3.40: 17313 3.40 - 4.00: 22277 4.00 - 4.60: 33932 Nonbonded interactions: 86488 Sorted by model distance: nonbonded pdb=" O ALA A 74 " pdb="HH22 ARG A 79 " model vdw 1.593 2.450 nonbonded pdb=" O LEU A 168 " pdb=" H ILE A 349 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU A 46 " pdb=" H ARG A 47 " model vdw 1.652 2.450 nonbonded pdb=" H ALA A 125 " pdb=" OD1 ASN A 128 " model vdw 1.675 2.450 nonbonded pdb=" O GLY A 12 " pdb=" HD1 HIS A 118 " model vdw 1.706 2.450 ... (remaining 86483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.070 3150 Z= 0.241 Angle : 0.729 14.259 4272 Z= 0.462 Chirality : 0.047 0.209 472 Planarity : 0.004 0.044 554 Dihedral : 16.505 88.465 1163 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.94 % Favored : 93.28 % Rotamer: Outliers : 0.89 % Allowed : 20.71 % Favored : 78.40 % Cbeta Deviations : 0.27 % 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: -0.46 (0.44), residues: 387 helix: 0.72 (0.46), residues: 148 sheet: -0.65 (0.74), residues: 55 loop : -1.01 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.002 0.001 HIS A 105 PHE 0.045 0.002 PHE A 210 TYR 0.006 0.001 TYR A 253 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.20046 ( 127) hydrogen bonds : angle 7.87130 ( 357) covalent geometry : bond 0.00408 ( 3150) covalent geometry : angle 0.72904 ( 4272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5729 (t80) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.3171 time to fit residues: 23.9464 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132443 restraints weight = 18181.250| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.83 r_work: 0.3730 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3150 Z= 0.141 Angle : 0.573 5.259 4272 Z= 0.309 Chirality : 0.044 0.154 472 Planarity : 0.005 0.044 554 Dihedral : 5.182 29.304 426 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.94 % Favored : 93.28 % Rotamer: Outliers : 1.78 % Allowed : 19.82 % Favored : 78.40 % 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: -0.35 (0.44), residues: 387 helix: 0.71 (0.43), residues: 156 sheet: -0.37 (0.78), residues: 55 loop : -0.99 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.005 0.001 HIS A 118 PHE 0.015 0.001 PHE A 210 TYR 0.016 0.001 TYR A 253 ARG 0.002 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 127) hydrogen bonds : angle 6.05013 ( 357) covalent geometry : bond 0.00310 ( 3150) covalent geometry : angle 0.57267 ( 4272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.3280 time to fit residues: 24.9569 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 362 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 24 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 = 0.4044 r_free = 0.4044 target = 0.150633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131271 restraints weight = 18489.995| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.85 r_work: 0.3702 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3150 Z= 0.159 Angle : 0.567 5.347 4272 Z= 0.303 Chirality : 0.044 0.148 472 Planarity : 0.005 0.044 554 Dihedral : 5.215 27.910 424 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.24 % Favored : 92.25 % Rotamer: Outliers : 2.37 % Allowed : 19.53 % Favored : 78.11 % 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: -0.59 (0.44), residues: 387 helix: 0.66 (0.43), residues: 157 sheet: -0.59 (0.74), residues: 60 loop : -1.28 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 410 HIS 0.008 0.001 HIS A 105 PHE 0.013 0.001 PHE A 262 TYR 0.010 0.001 TYR A 253 ARG 0.002 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 127) hydrogen bonds : angle 5.67766 ( 357) covalent geometry : bond 0.00353 ( 3150) covalent geometry : angle 0.56714 ( 4272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.7985 (mpp) cc_final: 0.7667 (mpp) REVERT: A 153 LYS cc_start: 0.8393 (mttm) cc_final: 0.7966 (mmtp) REVERT: A 216 GLU cc_start: 0.7646 (tt0) cc_final: 0.6952 (mp0) REVERT: A 263 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: A 282 MET cc_start: 0.4110 (mmp) cc_final: 0.3883 (mmm) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.3489 time to fit residues: 28.1215 Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.152198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132497 restraints weight = 18560.690| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.91 r_work: 0.3716 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3150 Z= 0.111 Angle : 0.526 4.852 4272 Z= 0.278 Chirality : 0.043 0.144 472 Planarity : 0.004 0.043 554 Dihedral : 4.983 25.790 424 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.72 % Favored : 92.76 % Rotamer: Outliers : 2.66 % Allowed : 22.19 % Favored : 75.15 % 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: -0.40 (0.45), residues: 387 helix: 0.83 (0.44), residues: 154 sheet: -0.55 (0.75), residues: 60 loop : -1.12 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.013 0.001 PHE A 262 TYR 0.005 0.001 TYR A 107 ARG 0.001 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 127) hydrogen bonds : angle 5.39663 ( 357) covalent geometry : bond 0.00257 ( 3150) covalent geometry : angle 0.52598 ( 4272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5802 (mmp-170) cc_final: 0.5497 (mmp-170) REVERT: A 90 ASN cc_start: 0.7975 (t0) cc_final: 0.7533 (t0) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.3491 time to fit residues: 27.3101 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 362 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.151945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132182 restraints weight = 18441.047| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.87 r_work: 0.3711 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3150 Z= 0.122 Angle : 0.521 4.757 4272 Z= 0.274 Chirality : 0.042 0.139 472 Planarity : 0.004 0.043 554 Dihedral : 4.924 24.091 424 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.46 % Favored : 93.02 % Rotamer: Outliers : 2.66 % Allowed : 21.89 % Favored : 75.44 % 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: -0.43 (0.45), residues: 387 helix: 0.85 (0.44), residues: 157 sheet: -0.64 (0.73), residues: 60 loop : -1.20 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 96 HIS 0.007 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.005 0.001 TYR A 107 ARG 0.001 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 127) hydrogen bonds : angle 5.23725 ( 357) covalent geometry : bond 0.00282 ( 3150) covalent geometry : angle 0.52080 ( 4272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5790 (mmp-170) cc_final: 0.5482 (mmp-170) REVERT: A 90 ASN cc_start: 0.7922 (t0) cc_final: 0.7695 (t0) REVERT: A 92 MET cc_start: 0.7961 (mpp) cc_final: 0.7697 (mpp) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.3305 time to fit residues: 27.6408 Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.151144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131550 restraints weight = 18204.971| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.81 r_work: 0.3705 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3150 Z= 0.131 Angle : 0.520 4.624 4272 Z= 0.274 Chirality : 0.043 0.140 472 Planarity : 0.005 0.045 554 Dihedral : 4.885 22.844 424 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 3.25 % Allowed : 21.89 % Favored : 74.85 % 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: -0.49 (0.45), residues: 387 helix: 0.84 (0.44), residues: 158 sheet: -0.84 (0.71), residues: 60 loop : -1.22 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 127) hydrogen bonds : angle 5.13041 ( 357) covalent geometry : bond 0.00299 ( 3150) covalent geometry : angle 0.51990 ( 4272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5703 (mmp-170) cc_final: 0.5355 (mmp-170) REVERT: A 90 ASN cc_start: 0.7895 (t0) cc_final: 0.7689 (t0) REVERT: A 92 MET cc_start: 0.7984 (mpp) cc_final: 0.7728 (mpp) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.3229 time to fit residues: 26.8214 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132330 restraints weight = 18444.856| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.84 r_work: 0.3710 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3150 Z= 0.115 Angle : 0.512 4.574 4272 Z= 0.268 Chirality : 0.042 0.136 472 Planarity : 0.004 0.044 554 Dihedral : 4.776 21.638 424 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 2.37 % Allowed : 22.78 % Favored : 74.85 % 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: -0.44 (0.45), residues: 387 helix: 0.93 (0.44), residues: 157 sheet: -0.84 (0.70), residues: 60 loop : -1.21 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 410 HIS 0.006 0.001 HIS A 105 PHE 0.011 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 127) hydrogen bonds : angle 5.05693 ( 357) covalent geometry : bond 0.00267 ( 3150) covalent geometry : angle 0.51181 ( 4272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5686 (mmp-170) cc_final: 0.5394 (mmp-170) REVERT: A 90 ASN cc_start: 0.7908 (t0) cc_final: 0.7509 (t0) REVERT: A 248 ARG cc_start: 0.6598 (tpt170) cc_final: 0.6398 (tpm170) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.3464 time to fit residues: 26.1373 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131902 restraints weight = 18241.692| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.82 r_work: 0.3704 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3150 Z= 0.126 Angle : 0.511 4.588 4272 Z= 0.268 Chirality : 0.043 0.138 472 Planarity : 0.004 0.045 554 Dihedral : 4.750 21.014 424 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 1.78 % Allowed : 22.49 % Favored : 75.74 % 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: -0.38 (0.45), residues: 387 helix: 1.22 (0.46), residues: 149 sheet: -0.97 (0.70), residues: 60 loop : -1.26 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.016 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 127) hydrogen bonds : angle 5.01080 ( 357) covalent geometry : bond 0.00290 ( 3150) covalent geometry : angle 0.51094 ( 4272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.0539 (OUTLIER) cc_final: 0.0237 (p) REVERT: A 47 ARG cc_start: 0.5750 (mmp-170) cc_final: 0.5444 (mmp-170) REVERT: A 90 ASN cc_start: 0.7900 (t0) cc_final: 0.7564 (t0) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.3624 time to fit residues: 30.5717 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131829 restraints weight = 18355.813| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.81 r_work: 0.3706 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3150 Z= 0.142 Angle : 0.522 4.560 4272 Z= 0.276 Chirality : 0.043 0.139 472 Planarity : 0.005 0.045 554 Dihedral : 4.797 21.001 424 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 2.37 % Allowed : 21.89 % Favored : 75.74 % 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: -0.46 (0.45), residues: 387 helix: 1.13 (0.45), residues: 149 sheet: -0.97 (0.69), residues: 60 loop : -1.29 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 96 HIS 0.006 0.001 HIS A 105 PHE 0.015 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 127) hydrogen bonds : angle 5.04153 ( 357) covalent geometry : bond 0.00324 ( 3150) covalent geometry : angle 0.52224 ( 4272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.0687 (OUTLIER) cc_final: 0.0391 (p) REVERT: A 47 ARG cc_start: 0.5735 (mmp-170) cc_final: 0.5435 (mmp-170) REVERT: A 70 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7758 (mm) REVERT: A 90 ASN cc_start: 0.7875 (t0) cc_final: 0.7545 (t0) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.3264 time to fit residues: 25.9229 Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.152002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132405 restraints weight = 18532.968| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.84 r_work: 0.3714 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3150 Z= 0.123 Angle : 0.511 4.520 4272 Z= 0.269 Chirality : 0.043 0.138 472 Planarity : 0.004 0.045 554 Dihedral : 4.711 20.264 424 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 1.78 % Allowed : 22.49 % Favored : 75.74 % 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: -0.51 (0.45), residues: 387 helix: 1.13 (0.45), residues: 149 sheet: -1.30 (0.66), residues: 66 loop : -1.21 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.005 0.001 HIS A 105 PHE 0.015 0.001 PHE A 262 TYR 0.007 0.001 TYR A 107 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 127) hydrogen bonds : angle 4.98381 ( 357) covalent geometry : bond 0.00284 ( 3150) covalent geometry : angle 0.51125 ( 4272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7747 (mm) REVERT: A 90 ASN cc_start: 0.7895 (t0) cc_final: 0.7627 (t0) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.3287 time to fit residues: 25.5954 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.152415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132872 restraints weight = 18588.805| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.85 r_work: 0.3720 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3150 Z= 0.113 Angle : 0.501 4.521 4272 Z= 0.262 Chirality : 0.042 0.137 472 Planarity : 0.004 0.045 554 Dihedral : 4.605 19.696 424 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Rotamer: Outliers : 1.78 % Allowed : 22.49 % Favored : 75.74 % 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: -0.42 (0.45), residues: 387 helix: 1.19 (0.45), residues: 149 sheet: -1.30 (0.66), residues: 66 loop : -1.13 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 410 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.001 PHE A 262 TYR 0.006 0.001 TYR A 107 ARG 0.001 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 127) hydrogen bonds : angle 4.89668 ( 357) covalent geometry : bond 0.00265 ( 3150) covalent geometry : angle 0.50081 ( 4272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.53 seconds wall clock time: 79 minutes 38.30 seconds (4778.30 seconds total)