Starting phenix.real_space_refine on Thu Mar 6 00:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.map" model { file = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p14_13155/03_2025/7p14_13155.cif" } resolution = 3.66 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= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 25 5.16 5 C 2533 2.51 5 N 579 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2706 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PLC': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 2.84, per 1000 atoms: 0.75 Number of scatterers: 3796 At special positions: 0 Unit cell: (96.348, 69.006, 70.308, 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 25 16.00 P 3 15.00 O 656 8.00 N 579 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 409.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 67.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.515A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.741A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.762A pdb=" N GLY A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.530A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 158 removed outlier: 3.590A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 3.572A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 removed outlier: 3.504A pdb=" N ARG A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 5.032A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 197 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 227 removed outlier: 3.654A pdb=" N LEU A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.535A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.733A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.233A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 Processing helix chain 'A' and resid 314 through 343 removed outlier: 3.616A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.778A pdb=" N TYR B 119 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.725A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 735 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: 0.94 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 545 1.32 - 1.44: 1168 1.44 - 1.56: 2136 1.56 - 1.69: 6 1.69 - 1.81: 37 Bond restraints: 3892 Sorted by residual: bond pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" C20 P5S A 403 " pdb=" C21 P5S A 403 " ideal model delta sigma weight residual 1.540 1.493 0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C4 PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C4 PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 PLC A 402 " pdb=" O3P PLC A 402 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5181 2.12 - 4.23: 75 4.23 - 6.35: 10 6.35 - 8.47: 2 8.47 - 10.58: 2 Bond angle restraints: 5270 Sorted by residual: angle pdb=" O3P PLC A 402 " pdb=" P PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 93.62 104.20 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 103.08 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C3 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 107.38 114.66 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" CA LYS A 284 " pdb=" CB LYS A 284 " pdb=" CG LYS A 284 " ideal model delta sigma weight residual 114.10 118.68 -4.58 2.00e+00 2.50e-01 5.24e+00 angle pdb=" CA LEU A 330 " pdb=" CB LEU A 330 " pdb=" CG LEU A 330 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.65e+00 ... (remaining 5265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2099 27.26 - 54.52: 136 54.52 - 81.77: 21 81.77 - 109.03: 8 109.03 - 136.29: 3 Dihedral angle restraints: 2267 sinusoidal: 938 harmonic: 1329 Sorted by residual: dihedral pdb=" O2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 304.29 168.00 136.29 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 67.16 -58.95 126.11 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C21 P5S A 403 " pdb=" C22 P5S A 403 " pdb=" C23 P5S A 403 " pdb=" C24 P5S A 403 " ideal model delta sinusoidal sigma weight residual 295.37 174.71 120.66 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 2264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 507 0.053 - 0.106: 73 0.106 - 0.159: 5 0.159 - 0.213: 0 0.213 - 0.266: 2 Chirality restraints: 587 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.05 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 P5S A 403 " pdb=" C1 P5S A 403 " pdb=" C3 P5S A 403 " pdb=" O37 P5S A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.33 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" C PRO A 201 " pdb=" CB PRO A 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 584 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 319 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 320 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 200 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 201 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 33 " -0.005 2.00e-02 2.50e+03 9.48e-03 8.99e-01 pdb=" C ASN B 33 " 0.016 2.00e-02 2.50e+03 pdb=" O ASN B 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE B 34 " -0.005 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1090 2.82 - 3.34: 3666 3.34 - 3.86: 5942 3.86 - 4.38: 7105 4.38 - 4.90: 12065 Nonbonded interactions: 29868 Sorted by model distance: nonbonded pdb=" OE1 GLU A 260 " pdb=" NH2 ARG A 264 " model vdw 2.295 3.120 nonbonded pdb=" O ILE A 16 " pdb=" OG1 THR A 20 " model vdw 2.369 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O LEU A 371 " model vdw 2.372 3.040 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.393 3.040 nonbonded pdb=" OH TYR A 208 " pdb=" OH TYR A 291 " model vdw 2.419 3.040 ... (remaining 29863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.180 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 0.047 3892 Z= 0.294 Angle : 0.627 10.583 5270 Z= 0.286 Chirality : 0.039 0.266 587 Planarity : 0.004 0.064 624 Dihedral : 19.089 136.288 1418 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.11 (0.40), residues: 444 helix: 1.37 (0.31), residues: 257 sheet: 1.11 (0.70), residues: 52 loop : -0.55 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.005 0.001 PHE A 225 TYR 0.015 0.001 TYR A 340 ARG 0.002 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.412 Fit side-chains REVERT: A 139 THR cc_start: 0.9153 (m) cc_final: 0.8884 (p) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1421 time to fit residues: 13.0813 Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 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 150 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.166213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134295 restraints weight = 4371.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137474 restraints weight = 2898.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139997 restraints weight = 2225.664| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3892 Z= 0.209 Angle : 0.603 9.719 5270 Z= 0.298 Chirality : 0.039 0.143 587 Planarity : 0.004 0.039 624 Dihedral : 18.301 129.435 623 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.01 % Allowed : 7.30 % Favored : 91.69 % 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: 2.03 (0.39), residues: 444 helix: 2.36 (0.29), residues: 265 sheet: 0.34 (0.69), residues: 57 loop : -0.41 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS A 344 PHE 0.034 0.002 PHE A 94 TYR 0.015 0.001 TYR A 291 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.446 Fit side-chains REVERT: A 50 CYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7525 (m) REVERT: A 130 ASP cc_start: 0.8947 (t0) cc_final: 0.8724 (t70) REVERT: A 139 THR cc_start: 0.9148 (m) cc_final: 0.8842 (p) REVERT: A 252 GLN cc_start: 0.8279 (pm20) cc_final: 0.8038 (pt0) REVERT: B 127 GLN cc_start: 0.8482 (tp40) cc_final: 0.8218 (tp-100) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.1539 time to fit residues: 14.7014 Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 83 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.167986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136905 restraints weight = 4428.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140067 restraints weight = 2999.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142346 restraints weight = 2309.917| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3892 Z= 0.255 Angle : 0.585 9.370 5270 Z= 0.290 Chirality : 0.041 0.201 587 Planarity : 0.003 0.036 624 Dihedral : 17.780 128.721 623 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.77 % Allowed : 9.07 % Favored : 88.16 % 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: 2.36 (0.40), residues: 444 helix: 2.67 (0.29), residues: 265 sheet: 0.98 (0.69), residues: 52 loop : -0.64 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 245 HIS 0.001 0.001 HIS A 344 PHE 0.024 0.002 PHE A 104 TYR 0.019 0.001 TYR A 343 ARG 0.005 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.379 Fit side-chains REVERT: A 7 ASN cc_start: 0.8912 (t0) cc_final: 0.8664 (m-40) REVERT: A 130 ASP cc_start: 0.8952 (t0) cc_final: 0.8673 (t0) REVERT: A 137 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: A 232 LEU cc_start: 0.8434 (mp) cc_final: 0.8158 (mp) REVERT: A 258 SER cc_start: 0.8887 (t) cc_final: 0.8620 (p) REVERT: B 127 GLN cc_start: 0.8458 (tp40) cc_final: 0.8197 (tp-100) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.1265 time to fit residues: 13.1020 Evaluate side-chains 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.166738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135477 restraints weight = 4395.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138802 restraints weight = 2957.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141122 restraints weight = 2269.489| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3892 Z= 0.189 Angle : 0.539 8.527 5270 Z= 0.267 Chirality : 0.039 0.198 587 Planarity : 0.003 0.032 624 Dihedral : 17.216 126.701 623 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.27 % Allowed : 11.59 % Favored : 86.15 % 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: 2.60 (0.40), residues: 444 helix: 2.96 (0.29), residues: 264 sheet: 0.89 (0.68), residues: 52 loop : -0.67 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 245 HIS 0.001 0.000 HIS A 250 PHE 0.014 0.001 PHE A 94 TYR 0.014 0.001 TYR A 343 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.418 Fit side-chains REVERT: A 130 ASP cc_start: 0.8740 (t0) cc_final: 0.8370 (t0) REVERT: A 137 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: A 258 SER cc_start: 0.8892 (t) cc_final: 0.8660 (p) REVERT: A 264 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7415 (ttm170) REVERT: B 127 GLN cc_start: 0.8377 (tp40) cc_final: 0.8132 (tp-100) outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 0.1466 time to fit residues: 14.3488 Evaluate side-chains 70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136105 restraints weight = 4512.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139320 restraints weight = 3041.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141657 restraints weight = 2339.053| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3892 Z= 0.256 Angle : 0.577 8.758 5270 Z= 0.286 Chirality : 0.040 0.200 587 Planarity : 0.003 0.027 624 Dihedral : 17.100 126.828 623 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.27 % Allowed : 12.34 % Favored : 85.39 % 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: 2.52 (0.40), residues: 444 helix: 2.91 (0.29), residues: 263 sheet: 0.91 (0.67), residues: 52 loop : -0.74 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.001 0.001 HIS A 250 PHE 0.019 0.001 PHE A 8 TYR 0.027 0.001 TYR A 343 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.388 Fit side-chains REVERT: A 130 ASP cc_start: 0.8807 (t0) cc_final: 0.8425 (t0) REVERT: A 258 SER cc_start: 0.8890 (t) cc_final: 0.8656 (p) REVERT: A 265 LEU cc_start: 0.8752 (tp) cc_final: 0.8493 (tt) REVERT: B 127 GLN cc_start: 0.8424 (tp40) cc_final: 0.8171 (tp-100) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.1379 time to fit residues: 12.8218 Evaluate side-chains 72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136444 restraints weight = 4388.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139744 restraints weight = 2958.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142044 restraints weight = 2270.863| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3892 Z= 0.201 Angle : 0.547 8.271 5270 Z= 0.271 Chirality : 0.039 0.199 587 Planarity : 0.003 0.041 624 Dihedral : 16.754 125.778 623 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.52 % Allowed : 13.10 % Favored : 84.38 % 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: 2.60 (0.40), residues: 444 helix: 3.00 (0.29), residues: 263 sheet: 0.91 (0.67), residues: 52 loop : -0.73 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 245 HIS 0.001 0.000 HIS A 250 PHE 0.015 0.001 PHE A 104 TYR 0.019 0.001 TYR A 343 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.383 Fit side-chains REVERT: A 130 ASP cc_start: 0.8732 (t0) cc_final: 0.8320 (t0) REVERT: A 199 PHE cc_start: 0.7649 (t80) cc_final: 0.7158 (t80) REVERT: A 258 SER cc_start: 0.8792 (t) cc_final: 0.8586 (p) REVERT: B 127 GLN cc_start: 0.8398 (tp40) cc_final: 0.8119 (tp-100) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1304 time to fit residues: 11.9742 Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137948 restraints weight = 4399.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140917 restraints weight = 2992.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143437 restraints weight = 2327.320| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3892 Z= 0.229 Angle : 0.566 8.259 5270 Z= 0.282 Chirality : 0.040 0.209 587 Planarity : 0.003 0.052 624 Dihedral : 16.527 125.337 623 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.53 % Allowed : 14.11 % Favored : 82.37 % 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: 2.55 (0.40), residues: 444 helix: 2.94 (0.29), residues: 263 sheet: 0.93 (0.67), residues: 52 loop : -0.75 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 250 PHE 0.015 0.001 PHE A 104 TYR 0.017 0.001 TYR A 343 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.377 Fit side-chains REVERT: A 1 MET cc_start: 0.7909 (tmm) cc_final: 0.7642 (tmm) REVERT: A 130 ASP cc_start: 0.8747 (t0) cc_final: 0.8314 (t0) REVERT: A 199 PHE cc_start: 0.7716 (t80) cc_final: 0.7209 (t80) REVERT: A 259 MET cc_start: 0.7949 (tpp) cc_final: 0.7295 (tpp) REVERT: A 265 LEU cc_start: 0.8610 (tp) cc_final: 0.8408 (tt) REVERT: B 127 GLN cc_start: 0.8413 (tp40) cc_final: 0.8135 (tp-100) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1261 time to fit residues: 12.1305 Evaluate side-chains 74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.170167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139266 restraints weight = 4441.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142632 restraints weight = 2987.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144688 restraints weight = 2285.942| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3892 Z= 0.195 Angle : 0.559 8.105 5270 Z= 0.280 Chirality : 0.039 0.212 587 Planarity : 0.003 0.032 624 Dihedral : 16.212 124.517 623 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.02 % Allowed : 16.37 % Favored : 80.60 % 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: 2.51 (0.39), residues: 444 helix: 2.91 (0.29), residues: 263 sheet: 0.92 (0.67), residues: 52 loop : -0.75 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 93 HIS 0.001 0.000 HIS A 101 PHE 0.016 0.001 PHE A 104 TYR 0.016 0.001 TYR A 343 ARG 0.010 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.414 Fit side-chains REVERT: A 1 MET cc_start: 0.8008 (tmm) cc_final: 0.7686 (tmm) REVERT: A 130 ASP cc_start: 0.8692 (t0) cc_final: 0.8250 (t0) REVERT: A 199 PHE cc_start: 0.7718 (t80) cc_final: 0.7218 (t80) REVERT: A 265 LEU cc_start: 0.8577 (tp) cc_final: 0.8371 (tt) REVERT: B 127 GLN cc_start: 0.8422 (tp40) cc_final: 0.8136 (tp-100) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.1398 time to fit residues: 13.2547 Evaluate side-chains 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0040 chunk 40 optimal weight: 0.3980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.170610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139521 restraints weight = 4367.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142886 restraints weight = 2954.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144902 restraints weight = 2274.463| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3892 Z= 0.170 Angle : 0.542 7.979 5270 Z= 0.270 Chirality : 0.039 0.210 587 Planarity : 0.003 0.025 624 Dihedral : 15.700 123.295 623 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.27 % Allowed : 16.88 % Favored : 79.85 % 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: 2.59 (0.40), residues: 444 helix: 3.04 (0.29), residues: 262 sheet: 0.47 (0.66), residues: 57 loop : -0.66 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 93 HIS 0.001 0.000 HIS A 101 PHE 0.017 0.001 PHE A 104 TYR 0.017 0.001 TYR A 340 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.545 Fit side-chains REVERT: A 1 MET cc_start: 0.7953 (tmm) cc_final: 0.7664 (tmm) REVERT: A 130 ASP cc_start: 0.8640 (t0) cc_final: 0.8195 (t0) REVERT: A 199 PHE cc_start: 0.7893 (t80) cc_final: 0.7412 (t80) REVERT: A 366 ARG cc_start: 0.6049 (ttm170) cc_final: 0.5824 (ttm-80) REVERT: B 127 GLN cc_start: 0.8413 (tp40) cc_final: 0.8117 (tp-100) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1712 time to fit residues: 17.8580 Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137323 restraints weight = 4485.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140450 restraints weight = 3019.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143060 restraints weight = 2327.253| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3892 Z= 0.195 Angle : 0.558 8.112 5270 Z= 0.277 Chirality : 0.039 0.212 587 Planarity : 0.003 0.032 624 Dihedral : 15.412 122.734 623 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.77 % Allowed : 17.13 % Favored : 80.10 % 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: 2.57 (0.40), residues: 444 helix: 3.01 (0.29), residues: 262 sheet: 0.48 (0.66), residues: 57 loop : -0.66 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 104 TYR 0.016 0.001 TYR A 343 ARG 0.004 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.445 Fit side-chains REVERT: A 1 MET cc_start: 0.7930 (tmm) cc_final: 0.7686 (tmm) REVERT: A 130 ASP cc_start: 0.8653 (t0) cc_final: 0.8253 (t0) REVERT: A 199 PHE cc_start: 0.7910 (t80) cc_final: 0.7410 (t80) REVERT: B 127 GLN cc_start: 0.8411 (tp40) cc_final: 0.8119 (tp-100) outliers start: 11 outliers final: 11 residues processed: 73 average time/residue: 0.1391 time to fit residues: 13.4731 Evaluate side-chains 78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136337 restraints weight = 4377.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139525 restraints weight = 2973.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141452 restraints weight = 2305.191| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3892 Z= 0.233 Angle : 0.578 8.202 5270 Z= 0.287 Chirality : 0.040 0.220 587 Planarity : 0.003 0.039 624 Dihedral : 15.356 123.147 623 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.02 % Allowed : 17.38 % Favored : 79.60 % 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: 2.52 (0.40), residues: 444 helix: 2.94 (0.29), residues: 262 sheet: 0.48 (0.66), residues: 57 loop : -0.61 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 104 TYR 0.027 0.001 TYR A 340 ARG 0.005 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.97 seconds wall clock time: 32 minutes 9.25 seconds (1929.25 seconds total)