Starting phenix.real_space_refine on Tue Feb 11 05:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk2_25170/02_2025/7sk2_25170.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 2788 2.51 5 N 651 2.21 5 O 703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4177 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4152 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 509} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.10, per 1000 atoms: 0.74 Number of scatterers: 4177 At special positions: 0 Unit cell: (83.739, 73.17, 77.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 703 8.00 N 651 7.00 C 2788 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 421.1 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: 30 helices and 1 sheets defined 75.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.559A pdb=" N MET A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.927A pdb=" N LEU A 118 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 153 removed outlier: 4.167A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.758A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.646A pdb=" N TRP A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.791A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.940A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 4.106A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 315 through 349 removed outlier: 3.501A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.522A pdb=" N VAL A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 410 removed outlier: 3.919A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 431 through 440 removed outlier: 6.303A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 476 through 489 removed outlier: 4.423A pdb=" N ASP A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 502 Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.559A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.235A pdb=" N ARG A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 256 hydrogen bonds defined for protein. 750 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: 1.18 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1211 1.34 - 1.46: 1142 1.46 - 1.58: 1904 1.58 - 1.70: 4 1.70 - 1.82: 52 Bond restraints: 4313 Sorted by residual: bond pdb=" C03 TGI A 601 " pdb=" C07 TGI A 601 " ideal model delta sigma weight residual 1.468 1.538 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C03 TGI A 601 " pdb=" S04 TGI A 601 " ideal model delta sigma weight residual 1.744 1.690 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C07 TGI A 601 " pdb=" C20 TGI A 601 " ideal model delta sigma weight residual 1.480 1.531 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C20 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.737 1.687 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C14 TGI A 601 " pdb=" C15 TGI A 601 " ideal model delta sigma weight residual 1.539 1.494 0.045 2.00e-02 2.50e+03 4.98e+00 ... (remaining 4308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 5608 2.19 - 4.38: 209 4.38 - 6.58: 43 6.58 - 8.77: 16 8.77 - 10.96: 7 Bond angle restraints: 5883 Sorted by residual: angle pdb=" C ILE A 377 " pdb=" N SER A 378 " pdb=" CA SER A 378 " ideal model delta sigma weight residual 120.58 127.09 -6.51 1.32e+00 5.74e-01 2.43e+01 angle pdb=" CB LYS A 350 " pdb=" CG LYS A 350 " pdb=" CD LYS A 350 " ideal model delta sigma weight residual 111.30 122.26 -10.96 2.30e+00 1.89e-01 2.27e+01 angle pdb=" CA VAL A 58 " pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 110.40 117.16 -6.76 1.70e+00 3.46e-01 1.58e+01 angle pdb=" C SER A 302 " pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C LEU A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta sigma weight residual 122.06 115.23 6.83 1.86e+00 2.89e-01 1.35e+01 ... (remaining 5878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2204 16.93 - 33.86: 179 33.86 - 50.80: 45 50.80 - 67.73: 4 67.73 - 84.66: 4 Dihedral angle restraints: 2436 sinusoidal: 906 harmonic: 1530 Sorted by residual: dihedral pdb=" CA PHE A 480 " pdb=" C PHE A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+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 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 379 0.039 - 0.079: 170 0.079 - 0.118: 60 0.118 - 0.157: 24 0.157 - 0.197: 9 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE A 341 " pdb=" CA ILE A 341 " pdb=" CG1 ILE A 341 " pdb=" CG2 ILE A 341 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA SER A 378 " pdb=" N SER A 378 " pdb=" C SER A 378 " pdb=" CB SER A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 639 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN A 137 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 136 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 138 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C ILE A 138 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 138 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 139 " 0.017 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 815 2.77 - 3.30: 4247 3.30 - 3.83: 7327 3.83 - 4.37: 8299 4.37 - 4.90: 13716 Nonbonded interactions: 34404 Sorted by model distance: nonbonded pdb=" OH TYR A 296 " pdb=" OG SER A 328 " model vdw 2.235 3.040 nonbonded pdb=" O VAL A 142 " pdb=" OG SER A 145 " model vdw 2.250 3.040 nonbonded pdb=" O PHE A 92 " pdb=" OG1 THR A 504 " model vdw 2.264 3.040 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.265 3.040 nonbonded pdb=" O SER A 437 " pdb=" OG1 THR A 440 " model vdw 2.285 3.040 ... (remaining 34399 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 0.070 4313 Z= 0.338 Angle : 1.059 10.959 5883 Z= 0.545 Chirality : 0.055 0.197 642 Planarity : 0.006 0.044 722 Dihedral : 13.666 84.661 1461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.34), residues: 530 helix: -1.32 (0.26), residues: 346 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.037 0.003 PHE A 480 TYR 0.039 0.003 TYR A 452 ARG 0.005 0.001 ARG A 195 *********************** 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 135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7822 (tmm) cc_final: 0.7527 (tmm) REVERT: A 283 GLU cc_start: 0.8133 (pp20) cc_final: 0.7926 (pp20) REVERT: A 292 ILE cc_start: 0.8583 (mm) cc_final: 0.8317 (mm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1372 time to fit residues: 23.8419 Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 196 ASN A 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.160640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.137479 restraints weight = 9148.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141504 restraints weight = 5412.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144254 restraints weight = 3701.005| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4313 Z= 0.234 Angle : 0.719 7.802 5883 Z= 0.374 Chirality : 0.043 0.146 642 Planarity : 0.005 0.031 722 Dihedral : 6.675 44.938 599 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.82 % Allowed : 11.74 % Favored : 85.45 % 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: -1.65 (0.37), residues: 530 helix: -0.66 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -1.82 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 230 HIS 0.009 0.003 HIS A 347 PHE 0.017 0.002 PHE A 462 TYR 0.024 0.002 TYR A 139 ARG 0.004 0.001 ARG A 566 *********************** 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 140 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8282 (m-40) cc_final: 0.7728 (m-40) REVERT: A 174 PHE cc_start: 0.5868 (p90) cc_final: 0.5653 (p90) REVERT: A 179 MET cc_start: 0.4210 (pmm) cc_final: 0.4008 (pmm) REVERT: A 200 MET cc_start: 0.6712 (tpt) cc_final: 0.6307 (mmm) REVERT: A 283 GLU cc_start: 0.8197 (pp20) cc_final: 0.7482 (pp20) REVERT: A 287 ASP cc_start: 0.7988 (m-30) cc_final: 0.7722 (m-30) REVERT: A 321 ILE cc_start: 0.8283 (pt) cc_final: 0.8080 (pt) REVERT: A 479 ARG cc_start: 0.7607 (ptt180) cc_final: 0.7355 (ptt180) REVERT: A 527 TYR cc_start: 0.7536 (t80) cc_final: 0.7334 (t80) REVERT: A 545 MET cc_start: 0.8386 (mmt) cc_final: 0.8153 (mmt) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.1304 time to fit residues: 22.9327 Evaluate side-chains 128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.160968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138192 restraints weight = 9178.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.141753 restraints weight = 5784.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144335 restraints weight = 4135.153| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4313 Z= 0.212 Angle : 0.689 7.698 5883 Z= 0.354 Chirality : 0.043 0.187 642 Planarity : 0.004 0.028 722 Dihedral : 6.316 43.987 599 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.82 % Allowed : 18.31 % Favored : 78.87 % 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: -1.26 (0.37), residues: 530 helix: -0.41 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -1.55 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 193 HIS 0.009 0.003 HIS A 347 PHE 0.025 0.002 PHE A 385 TYR 0.021 0.002 TYR A 139 ARG 0.004 0.001 ARG A 566 *********************** 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 137 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.440 Fit side-chains REVERT: A 77 ASN cc_start: 0.8137 (m110) cc_final: 0.7770 (m-40) REVERT: A 198 HIS cc_start: 0.7505 (m90) cc_final: 0.6956 (m90) REVERT: A 200 MET cc_start: 0.6800 (tpt) cc_final: 0.6225 (mmm) REVERT: A 283 GLU cc_start: 0.8022 (pp20) cc_final: 0.7381 (pp20) REVERT: A 287 ASP cc_start: 0.7871 (m-30) cc_final: 0.7285 (m-30) REVERT: A 321 ILE cc_start: 0.8406 (pt) cc_final: 0.8113 (pt) REVERT: A 479 ARG cc_start: 0.7424 (ptt180) cc_final: 0.7154 (ptt180) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.1365 time to fit residues: 23.6353 Evaluate side-chains 125 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.0020 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138308 restraints weight = 9197.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141851 restraints weight = 5712.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144538 restraints weight = 4060.945| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.204 Angle : 0.685 7.541 5883 Z= 0.349 Chirality : 0.042 0.156 642 Planarity : 0.004 0.042 722 Dihedral : 6.187 42.902 599 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.82 % Allowed : 20.66 % Favored : 76.53 % 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: -1.02 (0.37), residues: 530 helix: -0.23 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.45 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 193 HIS 0.009 0.002 HIS A 347 PHE 0.018 0.002 PHE A 385 TYR 0.020 0.002 TYR A 139 ARG 0.002 0.000 ARG A 479 *********************** 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 133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.456 Fit side-chains REVERT: A 77 ASN cc_start: 0.8133 (m110) cc_final: 0.7838 (m-40) REVERT: A 168 TRP cc_start: 0.5986 (p90) cc_final: 0.5692 (p90) REVERT: A 283 GLU cc_start: 0.8027 (pp20) cc_final: 0.7424 (pp20) REVERT: A 287 ASP cc_start: 0.7837 (m-30) cc_final: 0.7291 (m-30) REVERT: A 321 ILE cc_start: 0.8425 (pt) cc_final: 0.8116 (pt) REVERT: A 450 PHE cc_start: 0.7989 (m-10) cc_final: 0.7555 (m-10) outliers start: 12 outliers final: 10 residues processed: 123 average time/residue: 0.1376 time to fit residues: 22.1323 Evaluate side-chains 126 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 196 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.156743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135904 restraints weight = 8962.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139591 restraints weight = 5065.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141969 restraints weight = 3390.108| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4313 Z= 0.430 Angle : 0.830 8.736 5883 Z= 0.433 Chirality : 0.048 0.226 642 Planarity : 0.005 0.039 722 Dihedral : 6.699 37.937 599 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.16 % Allowed : 22.54 % Favored : 72.30 % 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: -1.35 (0.37), residues: 530 helix: -0.61 (0.26), residues: 363 sheet: None (None), residues: 0 loop : -1.23 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 168 HIS 0.008 0.003 HIS A 347 PHE 0.025 0.002 PHE A 87 TYR 0.039 0.003 TYR A 152 ARG 0.004 0.001 ARG A 172 *********************** 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 145 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.452 Fit side-chains REVERT: A 77 ASN cc_start: 0.8546 (m-40) cc_final: 0.8167 (m-40) REVERT: A 283 GLU cc_start: 0.8326 (pp20) cc_final: 0.7607 (pp20) REVERT: A 287 ASP cc_start: 0.8152 (m-30) cc_final: 0.7436 (m-30) REVERT: A 321 ILE cc_start: 0.8448 (pt) cc_final: 0.7985 (pt) REVERT: A 370 GLU cc_start: 0.8242 (tp30) cc_final: 0.7836 (tp30) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 0.1211 time to fit residues: 20.4101 Evaluate side-chains 134 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.158337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136347 restraints weight = 9341.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.139880 restraints weight = 5746.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.141998 restraints weight = 4055.107| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4313 Z= 0.216 Angle : 0.698 8.077 5883 Z= 0.359 Chirality : 0.043 0.215 642 Planarity : 0.004 0.042 722 Dihedral : 6.211 37.365 599 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.46 % Allowed : 22.30 % Favored : 73.24 % 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: -1.10 (0.37), residues: 530 helix: -0.36 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.28 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.008 0.002 HIS A 347 PHE 0.018 0.002 PHE A 480 TYR 0.021 0.002 TYR A 139 ARG 0.002 0.000 ARG A 566 *********************** 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 144 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8169 (m110) cc_final: 0.7954 (m-40) REVERT: A 198 HIS cc_start: 0.7622 (m90) cc_final: 0.7262 (m90) REVERT: A 283 GLU cc_start: 0.8152 (pp20) cc_final: 0.7559 (pp20) REVERT: A 287 ASP cc_start: 0.7862 (m-30) cc_final: 0.7387 (m-30) REVERT: A 321 ILE cc_start: 0.8333 (pt) cc_final: 0.7969 (pt) REVERT: A 370 GLU cc_start: 0.8120 (tp30) cc_final: 0.7744 (tp30) REVERT: A 450 PHE cc_start: 0.8030 (m-10) cc_final: 0.7793 (m-10) REVERT: A 479 ARG cc_start: 0.7421 (ptt180) cc_final: 0.7158 (ptt180) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.1303 time to fit residues: 22.4167 Evaluate side-chains 132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 538 TRP 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 42 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.159063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137685 restraints weight = 8820.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141521 restraints weight = 4902.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144019 restraints weight = 3251.456| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4313 Z= 0.304 Angle : 0.776 8.747 5883 Z= 0.397 Chirality : 0.046 0.196 642 Planarity : 0.004 0.044 722 Dihedral : 6.331 36.483 599 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.40 % Allowed : 24.18 % Favored : 70.42 % 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: -1.15 (0.37), residues: 530 helix: -0.38 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.34 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 193 HIS 0.008 0.003 HIS A 347 PHE 0.018 0.002 PHE A 87 TYR 0.027 0.002 TYR A 152 ARG 0.009 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 141 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8449 (m-40) cc_final: 0.8086 (m-40) REVERT: A 283 GLU cc_start: 0.8385 (pp20) cc_final: 0.7689 (pp20) REVERT: A 287 ASP cc_start: 0.8127 (m-30) cc_final: 0.7434 (m-30) REVERT: A 296 TYR cc_start: 0.7546 (m-10) cc_final: 0.7317 (m-10) REVERT: A 321 ILE cc_start: 0.8331 (pt) cc_final: 0.7949 (pt) outliers start: 23 outliers final: 19 residues processed: 126 average time/residue: 0.1415 time to fit residues: 23.0056 Evaluate side-chains 136 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.163750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142406 restraints weight = 8606.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.145863 restraints weight = 4911.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148632 restraints weight = 3399.193| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4313 Z= 0.221 Angle : 0.752 9.946 5883 Z= 0.378 Chirality : 0.044 0.191 642 Planarity : 0.004 0.035 722 Dihedral : 6.148 35.259 599 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.23 % Allowed : 24.88 % Favored : 70.89 % 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: -0.84 (0.37), residues: 530 helix: -0.13 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -1.22 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.010 0.003 HIS A 347 PHE 0.035 0.002 PHE A 447 TYR 0.022 0.002 TYR A 139 ARG 0.001 0.000 ARG A 195 *********************** 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 136 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8205 (m110) cc_final: 0.7927 (m-40) REVERT: A 283 GLU cc_start: 0.8186 (pp20) cc_final: 0.7575 (pp20) REVERT: A 287 ASP cc_start: 0.7902 (m-30) cc_final: 0.7398 (m-30) REVERT: A 321 ILE cc_start: 0.8372 (pt) cc_final: 0.8042 (pt) REVERT: A 479 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7186 (ptt180) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.1418 time to fit residues: 22.7728 Evaluate side-chains 130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.166438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144973 restraints weight = 8543.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.148832 restraints weight = 4895.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151423 restraints weight = 3284.957| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4313 Z= 0.197 Angle : 0.752 10.198 5883 Z= 0.377 Chirality : 0.044 0.184 642 Planarity : 0.004 0.028 722 Dihedral : 5.993 35.599 599 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.99 % Allowed : 26.06 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.75 (0.37), residues: 530 helix: -0.01 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.019 0.002 PHE A 447 TYR 0.022 0.002 TYR A 139 ARG 0.006 0.000 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 135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8115 (pp20) cc_final: 0.7536 (pp20) REVERT: A 287 ASP cc_start: 0.7845 (m-30) cc_final: 0.7332 (m-30) REVERT: A 321 ILE cc_start: 0.8284 (pt) cc_final: 0.8031 (pt) REVERT: A 391 MET cc_start: 0.7665 (mtt) cc_final: 0.7415 (mtt) REVERT: A 479 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7156 (ptt180) outliers start: 17 outliers final: 15 residues processed: 126 average time/residue: 0.1478 time to fit residues: 24.2957 Evaluate side-chains 129 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.165743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144467 restraints weight = 8620.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.148402 restraints weight = 4902.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150912 restraints weight = 3253.052| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4313 Z= 0.215 Angle : 0.770 9.996 5883 Z= 0.385 Chirality : 0.045 0.246 642 Planarity : 0.004 0.027 722 Dihedral : 6.000 35.562 599 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.99 % Allowed : 26.53 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.77 (0.37), residues: 530 helix: -0.04 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 500 HIS 0.008 0.002 HIS A 347 PHE 0.024 0.002 PHE A 385 TYR 0.031 0.002 TYR A 551 ARG 0.001 0.000 ARG A 211 ********************** 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 130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8556 (m-40) cc_final: 0.8078 (m-40) REVERT: A 200 MET cc_start: 0.6933 (tpt) cc_final: 0.6724 (tpt) REVERT: A 283 GLU cc_start: 0.8322 (pp20) cc_final: 0.7712 (tm-30) REVERT: A 287 ASP cc_start: 0.8124 (m-30) cc_final: 0.7181 (m-30) REVERT: A 321 ILE cc_start: 0.8288 (pt) cc_final: 0.8051 (pt) REVERT: A 391 MET cc_start: 0.7719 (mtt) cc_final: 0.7471 (mtt) REVERT: A 479 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7160 (ptt180) outliers start: 17 outliers final: 16 residues processed: 120 average time/residue: 0.1407 time to fit residues: 21.7168 Evaluate side-chains 128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.146886 restraints weight = 8442.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.150757 restraints weight = 4823.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153254 restraints weight = 3207.975| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4313 Z= 0.197 Angle : 0.795 12.919 5883 Z= 0.392 Chirality : 0.045 0.247 642 Planarity : 0.004 0.027 722 Dihedral : 5.915 35.997 599 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.76 % Allowed : 27.23 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.63 (0.37), residues: 530 helix: 0.07 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.20 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 500 HIS 0.007 0.002 HIS A 347 PHE 0.031 0.002 PHE A 404 TYR 0.022 0.001 TYR A 139 ARG 0.011 0.001 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.51 seconds wall clock time: 28 minutes 49.17 seconds (1729.17 seconds total)