Starting phenix.real_space_refine on Thu Mar 6 01:51:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/03_2025/7y7v_33671.cif" } resolution = 2.2 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= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 2861 2.51 5 N 659 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4341 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4240 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 22, 'TRANS': 509} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 101 Unusual residues: {' CL': 1, 'NAG': 3} Classifications: {'undetermined': 4, 'water': 58} Link IDs: {None: 61} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.13, per 1000 atoms: 0.72 Number of scatterers: 4341 At special positions: 0 Unit cell: (69.28, 71.445, 97.425, 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) Cl 1 17.00 S 34 16.00 O 786 8.00 N 659 7.00 C 2861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 176 " " NAG A 703 " - " ASN A 184 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 487.6 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.531A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.702A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 removed outlier: 4.763A pdb=" N ALA A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.798A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 4.031A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.599A pdb=" N THR A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.709A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.996A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.615A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.664A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.727A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.900A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.775A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.262A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 530 through 546 removed outlier: 4.004A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 717 1.33 - 1.46: 1744 1.46 - 1.59: 1904 1.59 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 4419 Sorted by residual: bond pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.33e-02 5.65e+03 9.84e+00 bond pdb=" C ASP A 171 " pdb=" N ARG A 172 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.43e-02 4.89e+03 3.40e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5911 2.26 - 4.52: 96 4.52 - 6.78: 11 6.78 - 9.04: 1 9.04 - 11.30: 1 Bond angle restraints: 6020 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.60 -11.30 2.00e+00 2.50e-01 3.19e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.65 -8.15 1.70e+00 3.46e-01 2.30e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.67 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 119.43 114.55 4.88 1.21e+00 6.83e-01 1.63e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 111.28 115.47 -4.19 1.09e+00 8.42e-01 1.48e+01 ... (remaining 6015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2160 16.28 - 32.57: 264 32.57 - 48.85: 83 48.85 - 65.14: 19 65.14 - 81.42: 5 Dihedral angle restraints: 2531 sinusoidal: 999 harmonic: 1532 Sorted by residual: dihedral pdb=" CA GLY A 111 " pdb=" C GLY A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 667 0.283 - 0.565: 2 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.413: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.157 2.00e-02 2.50e+03 1.65e-01 3.38e+02 pdb=" CG ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.246 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.031 2.00e-02 2.50e+03 3.38e-02 1.42e+01 pdb=" CG ASN A 181 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.024 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN A 176 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.031 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 50 2.64 - 3.21: 4207 3.21 - 3.77: 7211 3.77 - 4.34: 10093 4.34 - 4.90: 15768 Nonbonded interactions: 37329 Sorted by model distance: nonbonded pdb=" O SER A 243 " pdb=" O HOH A 801 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR A 140 " pdb=" O HOH A 802 " model vdw 2.079 3.040 nonbonded pdb=" O MET A 570 " pdb=" O HOH A 803 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN A 184 " pdb=" O5 NAG A 703 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 564 " pdb=" OE1 GLN A 568 " model vdw 2.252 3.040 ... (remaining 37324 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: 0.490 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.005 0.054 4419 Z= 0.324 Angle : 0.726 11.299 6020 Z= 0.404 Chirality : 0.073 1.413 670 Planarity : 0.005 0.033 728 Dihedral : 16.081 81.423 1556 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 22.35 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.34), residues: 530 helix: 0.62 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.022 0.003 PHE A 339 TYR 0.024 0.002 TYR A 72 ARG 0.007 0.002 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.485 Fit side-chains REVERT: A 568 GLN cc_start: 0.7303 (mp10) cc_final: 0.6874 (tp40) outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 1.4028 time to fit residues: 100.6250 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098782 restraints weight = 4171.693| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.46 r_work: 0.3089 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4419 Z= 0.186 Angle : 0.577 6.897 6020 Z= 0.302 Chirality : 0.047 0.431 670 Planarity : 0.004 0.025 728 Dihedral : 6.266 56.421 641 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.20 % Allowed : 18.14 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.36), residues: 530 helix: 1.53 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.06 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE A 462 TYR 0.017 0.001 TYR A 72 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.431 Fit side-chains REVERT: A 184 ASN cc_start: 0.5683 (OUTLIER) cc_final: 0.5376 (m110) REVERT: A 380 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 568 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6757 (tp40) outliers start: 19 outliers final: 9 residues processed: 74 average time/residue: 1.0866 time to fit residues: 83.7019 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096546 restraints weight = 4121.393| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.46 r_work: 0.3051 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4419 Z= 0.228 Angle : 0.592 6.808 6020 Z= 0.313 Chirality : 0.047 0.353 670 Planarity : 0.004 0.034 728 Dihedral : 6.190 59.655 641 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.87 % Allowed : 17.04 % Favored : 78.10 % 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: 1.28 (0.36), residues: 530 helix: 1.56 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.08 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.019 0.002 PHE A 339 TYR 0.021 0.002 TYR A 72 ARG 0.003 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.432 Fit side-chains REVERT: A 231 LYS cc_start: 0.4808 (OUTLIER) cc_final: 0.4180 (pptt) REVERT: A 278 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8518 (tmtm) REVERT: A 380 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 559 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7042 (mp) REVERT: A 568 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6612 (tp40) outliers start: 22 outliers final: 11 residues processed: 74 average time/residue: 1.1534 time to fit residues: 88.7411 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.129150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096154 restraints weight = 4201.988| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.48 r_work: 0.3048 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4419 Z= 0.232 Angle : 0.601 7.020 6020 Z= 0.319 Chirality : 0.046 0.344 670 Planarity : 0.004 0.036 728 Dihedral : 5.605 42.749 641 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.65 % Allowed : 16.37 % Favored : 78.98 % 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: 1.31 (0.36), residues: 530 helix: 1.58 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.06 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.019 0.002 PHE A 339 TYR 0.020 0.002 TYR A 72 ARG 0.002 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.480 Fit side-chains REVERT: A 230 TRP cc_start: 0.5338 (OUTLIER) cc_final: 0.4435 (p-90) REVERT: A 231 LYS cc_start: 0.4903 (OUTLIER) cc_final: 0.4267 (pptt) REVERT: A 278 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8528 (tmtm) REVERT: A 380 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8266 (tp) REVERT: A 568 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6554 (tp-100) outliers start: 21 outliers final: 12 residues processed: 74 average time/residue: 1.1266 time to fit residues: 86.8156 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098484 restraints weight = 4267.364| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.49 r_work: 0.3083 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4419 Z= 0.175 Angle : 0.550 6.798 6020 Z= 0.286 Chirality : 0.044 0.270 670 Planarity : 0.004 0.041 728 Dihedral : 5.221 45.187 641 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.20 % Allowed : 16.59 % Favored : 79.20 % 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: 1.53 (0.36), residues: 530 helix: 1.74 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.05 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.017 0.001 TYR A 246 ARG 0.006 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.472 Fit side-chains REVERT: A 197 MET cc_start: 0.9257 (ttp) cc_final: 0.9026 (ttt) REVERT: A 230 TRP cc_start: 0.5339 (OUTLIER) cc_final: 0.4986 (t60) REVERT: A 231 LYS cc_start: 0.5043 (OUTLIER) cc_final: 0.4345 (pptt) REVERT: A 278 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8501 (tmtm) REVERT: A 380 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 568 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6406 (tp40) outliers start: 19 outliers final: 9 residues processed: 75 average time/residue: 1.1425 time to fit residues: 89.1363 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098464 restraints weight = 4249.125| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.49 r_work: 0.3086 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4419 Z= 0.176 Angle : 0.561 9.895 6020 Z= 0.292 Chirality : 0.047 0.447 670 Planarity : 0.004 0.039 728 Dihedral : 5.045 47.069 641 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 17.04 % Favored : 78.98 % 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: 1.58 (0.37), residues: 530 helix: 1.74 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.018 0.002 TYR A 72 ARG 0.006 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.531 Fit side-chains REVERT: A 197 MET cc_start: 0.9260 (ttp) cc_final: 0.9032 (ttt) REVERT: A 230 TRP cc_start: 0.5418 (OUTLIER) cc_final: 0.5119 (t60) REVERT: A 278 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8551 (tmtm) REVERT: A 380 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 574 SER cc_start: 0.7289 (t) cc_final: 0.7053 (p) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 1.9719 time to fit residues: 153.6135 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.0060 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100192 restraints weight = 4188.538| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.47 r_work: 0.3111 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4419 Z= 0.160 Angle : 0.537 8.434 6020 Z= 0.280 Chirality : 0.045 0.356 670 Planarity : 0.004 0.037 728 Dihedral : 4.948 48.646 641 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.76 % Allowed : 17.26 % Favored : 78.98 % 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: 1.73 (0.37), residues: 530 helix: 1.85 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.016 0.001 PHE A 462 TYR 0.017 0.001 TYR A 246 ARG 0.010 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9263 (ttp) cc_final: 0.9021 (ttt) REVERT: A 278 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8494 (tmtm) REVERT: A 380 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 574 SER cc_start: 0.7310 (t) cc_final: 0.7068 (p) outliers start: 17 outliers final: 12 residues processed: 73 average time/residue: 1.2235 time to fit residues: 93.2954 Evaluate side-chains 80 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100880 restraints weight = 4197.647| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.46 r_work: 0.3123 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4419 Z= 0.155 Angle : 0.527 8.158 6020 Z= 0.273 Chirality : 0.044 0.351 670 Planarity : 0.004 0.035 728 Dihedral : 4.873 50.864 641 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 17.04 % Favored : 78.98 % 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: 1.82 (0.36), residues: 530 helix: 1.89 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.82 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.000 HIS A 313 PHE 0.015 0.001 PHE A 462 TYR 0.016 0.001 TYR A 72 ARG 0.008 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 156 THR cc_start: 0.8277 (p) cc_final: 0.8038 (t) REVERT: A 197 MET cc_start: 0.9261 (ttp) cc_final: 0.9001 (ttt) REVERT: A 278 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8542 (tmtm) REVERT: A 380 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 414 ARG cc_start: 0.6556 (mtm-85) cc_final: 0.6298 (mtm-85) REVERT: A 574 SER cc_start: 0.7324 (t) cc_final: 0.7080 (p) outliers start: 18 outliers final: 11 residues processed: 83 average time/residue: 1.7014 time to fit residues: 145.8889 Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 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 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098529 restraints weight = 4188.287| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.47 r_work: 0.3086 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4419 Z= 0.183 Angle : 0.558 7.971 6020 Z= 0.288 Chirality : 0.046 0.369 670 Planarity : 0.004 0.034 728 Dihedral : 4.349 16.695 639 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % 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: 1.77 (0.36), residues: 530 helix: 1.83 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.76 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.019 0.002 TYR A 72 ARG 0.006 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9304 (ttp) cc_final: 0.9038 (ttt) REVERT: A 278 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8535 (tmtm) REVERT: A 380 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 568 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7027 (mt0) REVERT: A 574 SER cc_start: 0.7292 (t) cc_final: 0.7023 (p) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 1.2796 time to fit residues: 102.0875 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098448 restraints weight = 4108.790| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.46 r_work: 0.3085 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4419 Z= 0.197 Angle : 0.573 7.921 6020 Z= 0.297 Chirality : 0.046 0.291 670 Planarity : 0.004 0.035 728 Dihedral : 4.427 19.933 639 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.54 % Allowed : 17.04 % Favored : 79.42 % 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: 1.72 (0.37), residues: 530 helix: 1.79 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.77 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.019 0.002 TYR A 72 ARG 0.005 0.001 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9305 (ttp) cc_final: 0.9034 (ttt) REVERT: A 278 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8533 (tmtm) REVERT: A 380 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8235 (tp) REVERT: A 568 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7110 (mt0) REVERT: A 574 SER cc_start: 0.7286 (t) cc_final: 0.6988 (p) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 1.2384 time to fit residues: 97.6661 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095418 restraints weight = 4143.779| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.46 r_work: 0.3036 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4419 Z= 0.295 Angle : 0.649 8.679 6020 Z= 0.340 Chirality : 0.049 0.251 670 Planarity : 0.005 0.039 728 Dihedral : 4.636 19.401 639 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % 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: 1.40 (0.36), residues: 530 helix: 1.60 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.002 PHE A 386 TYR 0.023 0.002 TYR A 72 ARG 0.006 0.001 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.46 seconds wall clock time: 74 minutes 24.24 seconds (4464.24 seconds total)