Starting phenix.real_space_refine on Fri May 9 16:22:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrk_61758/05_2025/9jrk_61758_neut.cif" } resolution = 3.44 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= 0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2098 2.51 5 N 517 2.21 5 O 514 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-5687/modules/chem_data/mon_lib" Total number of atoms: 3139 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3106 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.81 Number of scatterers: 3139 At special positions: 0 Unit cell: (69, 67, 72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 514 8.00 N 517 7.00 C 2098 6.00 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: 0.88 Conformation dependent library (CDL) restraints added in 384.2 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A 701 " Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.909A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.534A pdb=" N THR A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 removed outlier: 3.644A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.921A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.610A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.707A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 264 through 295 removed outlier: 3.927A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 4.239A pdb=" N ALA A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.517A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.652A pdb=" N THR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 419 Processing helix chain 'A' and resid 427 through 445 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.521A pdb=" N ALA A 450 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 236 hydrogen bonds defined for protein. 705 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: 0.76 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 436 1.29 - 1.42: 980 1.42 - 1.55: 1796 1.55 - 1.68: 0 1.68 - 1.81: 16 Bond restraints: 3228 Sorted by residual: bond pdb=" N MTX A 701 " pdb=" C MTX A 701 " ideal model delta sigma weight residual 1.339 1.464 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C2 MTX A 701 " pdb=" NA2 MTX A 701 " ideal model delta sigma weight residual 1.341 1.448 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 MTX A 701 " pdb=" NA4 MTX A 701 " ideal model delta sigma weight residual 1.328 1.435 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C4 MTX A 701 " pdb=" C4A MTX A 701 " ideal model delta sigma weight residual 1.444 1.355 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C4A MTX A 701 " pdb=" C8A MTX A 701 " ideal model delta sigma weight residual 1.405 1.323 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 3223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 4323 2.76 - 5.53: 59 5.53 - 8.29: 13 8.29 - 11.06: 2 11.06 - 13.82: 3 Bond angle restraints: 4400 Sorted by residual: angle pdb=" C GLN A 63 " pdb=" CA GLN A 63 " pdb=" CB GLN A 63 " ideal model delta sigma weight residual 110.90 102.54 8.36 1.58e+00 4.01e-01 2.80e+01 angle pdb=" C9 MTX A 701 " pdb=" N10 MTX A 701 " pdb=" CM MTX A 701 " ideal model delta sigma weight residual 119.23 133.05 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C7 MTX A 701 " pdb=" C6 MTX A 701 " pdb=" C9 MTX A 701 " ideal model delta sigma weight residual 122.52 109.59 12.93 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C9 MTX A 701 " pdb=" C6 MTX A 701 " pdb=" N5 MTX A 701 " ideal model delta sigma weight residual 117.81 130.52 -12.71 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C GLU A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta sigma weight residual 120.44 115.65 4.79 1.36e+00 5.41e-01 1.24e+01 ... (remaining 4395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 1563 17.16 - 34.32: 208 34.32 - 51.47: 58 51.47 - 68.63: 8 68.63 - 85.79: 3 Dihedral angle restraints: 1840 sinusoidal: 704 harmonic: 1136 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" N LYS A 336 " pdb=" CA LYS A 336 " pdb=" CB LYS A 336 " pdb=" CG LYS A 336 " ideal model delta sinusoidal sigma weight residual -60.00 -117.89 57.89 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ASN A 306 " pdb=" CA ASN A 306 " pdb=" CB ASN A 306 " pdb=" CG ASN A 306 " ideal model delta sinusoidal sigma weight residual -60.00 -117.76 57.76 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 397 0.047 - 0.094: 93 0.094 - 0.140: 17 0.140 - 0.187: 2 0.187 - 0.233: 1 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL A 128 " pdb=" N VAL A 128 " pdb=" C VAL A 128 " pdb=" CB VAL A 128 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA LEU A 52 " pdb=" N LEU A 52 " pdb=" C LEU A 52 " pdb=" CB LEU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 507 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 358 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 359 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 447 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C PHE A 447 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 447 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 448 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 373 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ARG A 373 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 373 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 374 " -0.009 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 983 2.82 - 3.34: 3234 3.34 - 3.86: 5438 3.86 - 4.38: 6058 4.38 - 4.90: 10382 Nonbonded interactions: 26095 Sorted by model distance: nonbonded pdb=" OG SER A 271 " pdb=" OD1 ASN A 403 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A 75 " pdb=" OG SER A 127 " model vdw 2.307 3.040 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.339 3.040 nonbonded pdb=" N THR A 60 " pdb=" OE1 GLN A 63 " model vdw 2.344 3.120 nonbonded pdb=" OH TYR A 51 " pdb=" NZ LYS A 57 " model vdw 2.350 3.120 ... (remaining 26090 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: 0.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 3228 Z= 0.340 Angle : 0.864 13.824 4400 Z= 0.444 Chirality : 0.042 0.233 510 Planarity : 0.005 0.050 525 Dihedral : 16.861 85.788 1110 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 27.11 % Favored : 72.89 % 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: 0.28 (0.43), residues: 380 helix: 0.81 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -2.67 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.025 0.002 PHE A 84 TYR 0.011 0.001 TYR A 287 ARG 0.001 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.14170 ( 236) hydrogen bonds : angle 6.08231 ( 705) covalent geometry : bond 0.00620 ( 3228) covalent geometry : angle 0.86364 ( 4400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7993 (mmm160) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1894 time to fit residues: 10.3697 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115958 restraints weight = 3766.121| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.91 r_work: 0.3149 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3228 Z= 0.161 Angle : 0.587 11.778 4400 Z= 0.298 Chirality : 0.038 0.114 510 Planarity : 0.004 0.054 525 Dihedral : 8.866 84.026 443 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.31 % Allowed : 25.90 % Favored : 70.78 % 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: 0.73 (0.42), residues: 380 helix: 1.02 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.43 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.025 0.002 PHE A 84 TYR 0.011 0.001 TYR A 376 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 236) hydrogen bonds : angle 4.32961 ( 705) covalent geometry : bond 0.00365 ( 3228) covalent geometry : angle 0.58677 ( 4400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7591 (mmm160) REVERT: A 67 GLU cc_start: 0.7261 (mp0) cc_final: 0.7044 (mp0) REVERT: A 256 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7076 (mmp-170) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.1852 time to fit residues: 13.1117 Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.146965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118065 restraints weight = 3732.486| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.89 r_work: 0.3176 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3228 Z= 0.130 Angle : 0.537 10.587 4400 Z= 0.272 Chirality : 0.037 0.111 510 Planarity : 0.004 0.055 525 Dihedral : 8.563 80.960 443 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.52 % Allowed : 25.90 % Favored : 69.58 % 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: 1.11 (0.43), residues: 380 helix: 1.28 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.37 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 457 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 376 ARG 0.002 0.000 ARG A 61 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 236) hydrogen bonds : angle 4.10900 ( 705) covalent geometry : bond 0.00287 ( 3228) covalent geometry : angle 0.53707 ( 4400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7602 (mmm160) REVERT: A 67 GLU cc_start: 0.7330 (mp0) cc_final: 0.6855 (mp0) REVERT: A 97 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 256 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.7089 (mmp-170) REVERT: A 336 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8266 (mtmt) REVERT: A 417 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7242 (tt) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1623 time to fit residues: 12.5773 Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116419 restraints weight = 3769.660| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.89 r_work: 0.3142 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3228 Z= 0.156 Angle : 0.557 8.356 4400 Z= 0.283 Chirality : 0.039 0.271 510 Planarity : 0.004 0.056 525 Dihedral : 8.444 88.632 443 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.42 % Allowed : 25.90 % Favored : 68.67 % 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: 1.10 (0.43), residues: 380 helix: 1.29 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.48 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.001 HIS A 457 PHE 0.024 0.002 PHE A 84 TYR 0.012 0.001 TYR A 376 ARG 0.001 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 236) hydrogen bonds : angle 4.07929 ( 705) covalent geometry : bond 0.00357 ( 3228) covalent geometry : angle 0.55748 ( 4400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7505 (mmm160) REVERT: A 67 GLU cc_start: 0.7519 (mp0) cc_final: 0.6844 (mp0) REVERT: A 256 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7103 (mmp-170) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.1715 time to fit residues: 12.8940 Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.145282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116364 restraints weight = 3750.372| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.88 r_work: 0.3140 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3228 Z= 0.151 Angle : 0.552 6.755 4400 Z= 0.281 Chirality : 0.038 0.203 510 Planarity : 0.004 0.056 525 Dihedral : 8.102 85.174 443 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.61 % Allowed : 27.41 % Favored : 68.98 % 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: 1.27 (0.42), residues: 380 helix: 1.43 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -2.33 (0.69), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.025 0.001 PHE A 84 TYR 0.012 0.001 TYR A 376 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 236) hydrogen bonds : angle 4.04423 ( 705) covalent geometry : bond 0.00346 ( 3228) covalent geometry : angle 0.55219 ( 4400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7765 (mmm160) REVERT: A 67 GLU cc_start: 0.7625 (mp0) cc_final: 0.6821 (mp0) REVERT: A 256 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7133 (mmp-170) REVERT: A 417 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7229 (tt) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1627 time to fit residues: 11.6762 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 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 = 0.3620 r_free = 0.3620 target = 0.144874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115733 restraints weight = 3842.954| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.91 r_work: 0.3139 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3228 Z= 0.153 Angle : 0.558 8.070 4400 Z= 0.283 Chirality : 0.039 0.191 510 Planarity : 0.004 0.056 525 Dihedral : 7.924 82.622 443 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.52 % Allowed : 26.51 % Favored : 68.98 % 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: 1.24 (0.42), residues: 380 helix: 1.45 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -2.49 (0.71), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 236) hydrogen bonds : angle 4.01932 ( 705) covalent geometry : bond 0.00353 ( 3228) covalent geometry : angle 0.55775 ( 4400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7735 (mmm160) REVERT: A 67 GLU cc_start: 0.7611 (mp0) cc_final: 0.6811 (mp0) REVERT: A 256 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7128 (mmp-170) REVERT: A 417 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7197 (tt) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1534 time to fit residues: 11.0010 Evaluate side-chains 62 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.145114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116355 restraints weight = 3733.925| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.89 r_work: 0.3145 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3228 Z= 0.147 Angle : 0.555 6.975 4400 Z= 0.280 Chirality : 0.038 0.186 510 Planarity : 0.004 0.058 525 Dihedral : 7.774 80.086 443 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.22 % Allowed : 26.20 % Favored : 69.58 % 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: 1.38 (0.42), residues: 380 helix: 1.55 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -2.45 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 376 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 236) hydrogen bonds : angle 3.97820 ( 705) covalent geometry : bond 0.00338 ( 3228) covalent geometry : angle 0.55499 ( 4400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7548 (mmm160) REVERT: A 63 GLN cc_start: 0.8734 (mt0) cc_final: 0.8241 (pt0) REVERT: A 67 GLU cc_start: 0.7548 (mp0) cc_final: 0.6742 (mp0) REVERT: A 256 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7141 (mmp-170) REVERT: A 417 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7172 (tt) outliers start: 14 outliers final: 11 residues processed: 56 average time/residue: 0.1638 time to fit residues: 11.1466 Evaluate side-chains 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.144130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115380 restraints weight = 3769.124| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.88 r_work: 0.3133 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3228 Z= 0.159 Angle : 0.565 6.703 4400 Z= 0.286 Chirality : 0.038 0.183 510 Planarity : 0.004 0.058 525 Dihedral : 7.726 78.690 443 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.22 % Allowed : 26.51 % Favored : 69.28 % 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: 1.36 (0.42), residues: 380 helix: 1.53 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -2.36 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.024 0.002 PHE A 84 TYR 0.012 0.001 TYR A 287 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 236) hydrogen bonds : angle 3.98773 ( 705) covalent geometry : bond 0.00370 ( 3228) covalent geometry : angle 0.56538 ( 4400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7550 (mmm160) REVERT: A 63 GLN cc_start: 0.8751 (mt0) cc_final: 0.8254 (pt0) REVERT: A 67 GLU cc_start: 0.7607 (mp0) cc_final: 0.6790 (mp0) REVERT: A 80 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7726 (tp) REVERT: A 256 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7123 (mmp-170) REVERT: A 355 HIS cc_start: 0.6022 (t-90) cc_final: 0.5777 (t70) REVERT: A 417 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7187 (tt) outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.1679 time to fit residues: 11.3065 Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.147657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119280 restraints weight = 3775.705| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.90 r_work: 0.3190 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3228 Z= 0.117 Angle : 0.524 6.566 4400 Z= 0.264 Chirality : 0.037 0.176 510 Planarity : 0.004 0.059 525 Dihedral : 7.490 77.439 443 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.31 % Allowed : 27.71 % Favored : 68.98 % 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: 1.61 (0.43), residues: 380 helix: 1.65 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -2.28 (0.71), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.024 0.001 PHE A 416 TYR 0.013 0.001 TYR A 376 ARG 0.001 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 236) hydrogen bonds : angle 3.85344 ( 705) covalent geometry : bond 0.00256 ( 3228) covalent geometry : angle 0.52416 ( 4400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7527 (mmm160) REVERT: A 67 GLU cc_start: 0.7562 (mp0) cc_final: 0.6789 (mp0) REVERT: A 80 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 256 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7124 (mmp-170) REVERT: A 355 HIS cc_start: 0.5970 (t-90) cc_final: 0.5751 (t70) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1678 time to fit residues: 11.5009 Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.146770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118608 restraints weight = 3721.302| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.88 r_work: 0.3180 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3228 Z= 0.126 Angle : 0.541 8.020 4400 Z= 0.269 Chirality : 0.037 0.169 510 Planarity : 0.004 0.059 525 Dihedral : 7.449 77.454 443 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.01 % Allowed : 28.31 % Favored : 68.67 % 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: 1.59 (0.43), residues: 380 helix: 1.62 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.31 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.023 0.001 PHE A 416 TYR 0.012 0.001 TYR A 376 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 236) hydrogen bonds : angle 3.86005 ( 705) covalent geometry : bond 0.00284 ( 3228) covalent geometry : angle 0.54070 ( 4400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7571 (mmm160) REVERT: A 67 GLU cc_start: 0.7552 (mp0) cc_final: 0.6724 (mp0) REVERT: A 80 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7537 (tp) REVERT: A 256 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7122 (mmp-170) REVERT: A 355 HIS cc_start: 0.5941 (t-90) cc_final: 0.5726 (t70) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 0.1821 time to fit residues: 11.5910 Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 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 = 0.3631 r_free = 0.3631 target = 0.146606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117735 restraints weight = 3852.191| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.94 r_work: 0.3145 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3228 Z= 0.138 Angle : 0.558 7.808 4400 Z= 0.277 Chirality : 0.038 0.169 510 Planarity : 0.004 0.059 525 Dihedral : 7.448 77.601 443 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.01 % Allowed : 28.31 % Favored : 68.67 % 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: 1.55 (0.43), residues: 380 helix: 1.59 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.29 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.023 0.002 PHE A 416 TYR 0.012 0.001 TYR A 376 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 236) hydrogen bonds : angle 3.86442 ( 705) covalent geometry : bond 0.00314 ( 3228) covalent geometry : angle 0.55821 ( 4400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.00 seconds wall clock time: 33 minutes 49.29 seconds (2029.29 seconds total)