Starting phenix.real_space_refine on Fri Dec 27 11:29:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7v_33671/12_2024/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/12_2024/7y7v_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_33671/12_2024/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/12_2024/7y7v_33671.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/12_2024/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/12_2024/7y7v_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-5532/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: 3.25, per 1000 atoms: 0.75 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: 1.17 Conformation dependent library (CDL) restraints added in 535.4 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: 1.21 Time building geometry restraints manager: 1.28 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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 : 0.500 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: 1.1697 time to fit residues: 84.0610 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 : 0.528 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.532 Fit side-chains REVERT: A 380 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 19 outliers final: 9 residues processed: 74 average time/residue: 1.1373 time to fit residues: 87.6904 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4419 Z= 0.253 Angle : 0.608 6.802 6020 Z= 0.323 Chirality : 0.048 0.349 670 Planarity : 0.004 0.033 728 Dihedral : 6.092 52.233 641 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.42 % Allowed : 17.04 % Favored : 78.54 % 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: 1.23 (0.36), residues: 530 helix: 1.51 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.09 (0.48), residues: 143 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 0.020 0.002 PHE A 339 TYR 0.021 0.002 TYR A 72 ARG 0.003 0.001 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 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.869 Fit side-chains REVERT: A 231 LYS cc_start: 0.4167 (OUTLIER) cc_final: 0.3858 (pptt) REVERT: A 278 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8594 (tmtm) REVERT: A 380 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8265 (tp) REVERT: A 559 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7235 (mp) outliers start: 20 outliers final: 12 residues processed: 75 average time/residue: 1.2091 time to fit residues: 94.4214 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 117 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1551 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= 0.176 Angle : 0.546 6.768 6020 Z= 0.287 Chirality : 0.044 0.357 670 Planarity : 0.004 0.034 728 Dihedral : 5.542 42.853 641 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.98 % Allowed : 16.37 % Favored : 79.65 % 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: 1.54 (0.36), residues: 530 helix: 1.73 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.01 (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 0.016 0.001 TYR A 72 ARG 0.002 0.000 ARG A 414 *********************** 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 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.529 Fit side-chains REVERT: A 230 TRP cc_start: 0.5129 (OUTLIER) cc_final: 0.4519 (t60) REVERT: A 231 LYS cc_start: 0.4419 (OUTLIER) cc_final: 0.4076 (pptt) REVERT: A 278 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8623 (tmtm) REVERT: A 380 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8203 (tp) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 1.2265 time to fit residues: 91.8307 Evaluate side-chains 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR 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 564 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4419 Z= 0.270 Angle : 0.628 10.057 6020 Z= 0.327 Chirality : 0.049 0.320 670 Planarity : 0.004 0.039 728 Dihedral : 5.524 44.321 641 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.91 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: 1.31 (0.36), residues: 530 helix: 1.55 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.019 0.002 PHE A 339 TYR 0.023 0.002 TYR A 72 ARG 0.002 0.000 ARG A 351 *********************** 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 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.532 Fit side-chains REVERT: A 230 TRP cc_start: 0.5370 (OUTLIER) cc_final: 0.4305 (p-90) REVERT: A 278 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8626 (tmtm) REVERT: A 380 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8272 (tp) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 1.2725 time to fit residues: 93.8412 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 117 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 Chi-restraints excluded: chain A residue 564 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.9624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4419 Z= 0.314 Angle : 0.657 8.451 6020 Z= 0.349 Chirality : 0.051 0.441 670 Planarity : 0.005 0.064 728 Dihedral : 5.467 46.579 641 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.20 % Allowed : 17.04 % Favored : 78.76 % 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: 1.15 (0.36), residues: 530 helix: 1.42 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.99 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 116 HIS 0.003 0.001 HIS A 347 PHE 0.020 0.002 PHE A 339 TYR 0.023 0.003 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 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.500 Fit side-chains REVERT: A 197 MET cc_start: 0.9202 (ttp) cc_final: 0.8977 (ttt) REVERT: A 230 TRP cc_start: 0.5558 (OUTLIER) cc_final: 0.4375 (p-90) REVERT: A 278 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8609 (tmtm) REVERT: A 380 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8346 (tp) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 1.1460 time to fit residues: 85.8769 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1531 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= 0.194 Angle : 0.575 7.053 6020 Z= 0.303 Chirality : 0.047 0.392 670 Planarity : 0.004 0.041 728 Dihedral : 5.207 49.518 641 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 17.48 % Favored : 78.54 % 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: 1.49 (0.36), residues: 530 helix: 1.68 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.93 (0.51), residues: 141 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 0.019 0.002 PHE A 339 TYR 0.019 0.002 TYR A 246 ARG 0.007 0.001 ARG A 414 *********************** 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 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.508 Fit side-chains REVERT: A 230 TRP cc_start: 0.5446 (OUTLIER) cc_final: 0.4825 (t60) REVERT: A 278 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8617 (tmtm) REVERT: A 380 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8260 (tp) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 1.1812 time to fit residues: 86.1644 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 564 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4419 Z= 0.198 Angle : 0.577 6.772 6020 Z= 0.301 Chirality : 0.047 0.380 670 Planarity : 0.004 0.044 728 Dihedral : 5.076 51.785 641 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.32 % Allowed : 18.36 % Favored : 78.32 % 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: 1.59 (0.37), residues: 530 helix: 1.76 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.94 (0.51), residues: 140 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 0.019 0.002 PHE A 339 TYR 0.020 0.002 TYR A 246 ARG 0.007 0.001 ARG A 414 *********************** 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 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.552 Fit side-chains REVERT: A 278 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8600 (tmtm) REVERT: A 380 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8248 (tp) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 1.2756 time to fit residues: 89.5824 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 564 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4419 Z= 0.204 Angle : 0.577 6.781 6020 Z= 0.301 Chirality : 0.046 0.295 670 Planarity : 0.004 0.046 728 Dihedral : 5.098 54.660 641 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.54 % Allowed : 18.14 % Favored : 78.32 % 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: 1.60 (0.36), residues: 530 helix: 1.75 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.019 0.002 PHE A 339 TYR 0.022 0.002 TYR A 246 ARG 0.007 0.000 ARG A 414 *********************** 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 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.431 Fit side-chains REVERT: A 278 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8596 (tmtm) REVERT: A 380 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8249 (tp) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 1.3802 time to fit residues: 98.8005 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 564 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4419 Z= 0.254 Angle : 0.618 6.786 6020 Z= 0.326 Chirality : 0.047 0.242 670 Planarity : 0.004 0.045 728 Dihedral : 5.226 56.841 641 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.54 % Allowed : 18.14 % Favored : 78.32 % 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: 388 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.018 0.002 PHE A 339 TYR 0.027 0.002 TYR A 246 ARG 0.008 0.001 ARG A 414 ********************** 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 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.479 Fit side-chains REVERT: A 197 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8248 (ttt) REVERT: A 278 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8608 (tmtm) REVERT: A 380 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8288 (tp) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 1.3203 time to fit residues: 91.7073 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 230 TRP 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 564 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.128924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096162 restraints weight = 4179.012| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.47 r_work: 0.3051 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4419 Z= 0.235 Angle : 0.602 6.838 6020 Z= 0.316 Chirality : 0.046 0.234 670 Planarity : 0.004 0.048 728 Dihedral : 5.242 59.348 641 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.32 % Allowed : 18.14 % Favored : 78.54 % 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: 1.48 (0.36), residues: 530 helix: 1.66 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.93 (0.50), residues: 141 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 0.020 0.002 PHE A 339 TYR 0.030 0.002 TYR A 246 ARG 0.006 0.001 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.15 seconds wall clock time: 37 minutes 26.39 seconds (2246.39 seconds total)