Starting phenix.real_space_refine on Wed Jul 23 20:05:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk2_25170/07_2025/7sk2_25170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk2_25170/07_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_25170/07_2025/7sk2_25170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk2_25170/07_2025/7sk2_25170.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk2_25170/07_2025/7sk2_25170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk2_25170/07_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-5711/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: 4.34, per 1000 atoms: 1.04 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: 1.05 Conformation dependent library (CDL) restraints added in 629.3 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: 0.35 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: 1.85 Time building geometry restraints manager: 1.29 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.090 Find NCS groups from input model: 0.150 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:5.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- 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 4314 Z= 0.251 Angle : 1.059 10.959 5885 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 Details of bonding type rmsd hydrogen bonds : bond 0.17204 ( 256) hydrogen bonds : angle 7.92987 ( 750) SS BOND : bond 0.00056 ( 1) SS BOND : angle 1.06859 ( 2) covalent geometry : bond 0.00509 ( 4313) covalent geometry : angle 1.05876 ( 5883) *********************** 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 : 1.314 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: 0.1781 time to fit residues: 32.3814 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 : 1.178 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137520 restraints weight = 9148.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141485 restraints weight = 5396.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144280 restraints weight = 3705.823| |-----------------------------------------------------------------------------| 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 4314 Z= 0.170 Angle : 0.719 7.802 5885 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 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 256) hydrogen bonds : angle 5.89544 ( 750) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.96516 ( 2) covalent geometry : bond 0.00365 ( 4313) covalent geometry : angle 0.71920 ( 5883) *********************** 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 : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8284 (m-40) cc_final: 0.7727 (m-40) REVERT: A 174 PHE cc_start: 0.5862 (p90) cc_final: 0.5648 (p90) REVERT: A 179 MET cc_start: 0.4205 (pmm) cc_final: 0.4004 (pmm) REVERT: A 200 MET cc_start: 0.6713 (tpt) cc_final: 0.6309 (mmm) REVERT: A 283 GLU cc_start: 0.8195 (pp20) cc_final: 0.7480 (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: 0.7608 (ptt180) cc_final: 0.7354 (ptt180) REVERT: A 527 TYR cc_start: 0.7535 (t80) cc_final: 0.7333 (t80) REVERT: A 545 MET cc_start: 0.8383 (mmt) cc_final: 0.8148 (mmt) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.1231 time to fit residues: 21.5730 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 : 0.437 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 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 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 = 0.4170 r_free = 0.4170 target = 0.161776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139047 restraints weight = 9127.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142559 restraints weight = 5712.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.145226 restraints weight = 4100.653| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4314 Z= 0.146 Angle : 0.681 7.531 5885 Z= 0.350 Chirality : 0.043 0.182 642 Planarity : 0.004 0.028 722 Dihedral : 6.288 44.215 599 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.58 % Allowed : 18.08 % Favored : 79.34 % 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: -1.22 (0.37), residues: 530 helix: -0.38 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -1.55 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 256) hydrogen bonds : angle 5.50566 ( 750) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.79633 ( 2) covalent geometry : bond 0.00310 ( 4313) covalent geometry : angle 0.68109 ( 5883) *********************** 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 135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.461 Fit side-chains REVERT: A 77 ASN cc_start: 0.8130 (m110) cc_final: 0.7737 (m-40) REVERT: A 198 HIS cc_start: 0.7485 (m90) cc_final: 0.6917 (m90) REVERT: A 200 MET cc_start: 0.6810 (tpt) cc_final: 0.6594 (tpt) REVERT: A 269 LEU cc_start: 0.7651 (mm) cc_final: 0.7448 (mm) REVERT: A 283 GLU cc_start: 0.8023 (pp20) cc_final: 0.7372 (pp20) REVERT: A 287 ASP cc_start: 0.7856 (m-30) cc_final: 0.7289 (m-30) REVERT: A 321 ILE cc_start: 0.8392 (pt) cc_final: 0.8106 (pt) REVERT: A 479 ARG cc_start: 0.7431 (ptt180) cc_final: 0.7179 (ptt180) outliers start: 11 outliers final: 9 residues processed: 129 average time/residue: 0.1246 time to fit residues: 21.2061 Evaluate side-chains 124 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 26 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- 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 A 438 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.163651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140779 restraints weight = 9159.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144476 restraints weight = 5683.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.147188 restraints weight = 4023.004| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4314 Z= 0.130 Angle : 0.670 7.683 5885 Z= 0.340 Chirality : 0.041 0.147 642 Planarity : 0.004 0.038 722 Dihedral : 6.108 43.785 599 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.82 % Allowed : 20.42 % Favored : 76.76 % 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: -0.80 (0.37), residues: 530 helix: -0.02 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.40 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.008 0.002 HIS A 347 PHE 0.020 0.002 PHE A 385 TYR 0.018 0.002 TYR A 139 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 256) hydrogen bonds : angle 5.35386 ( 750) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.76757 ( 2) covalent geometry : bond 0.00274 ( 4313) covalent geometry : angle 0.67009 ( 5883) *********************** 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 138 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.474 Fit side-chains REVERT: A 77 ASN cc_start: 0.8100 (m110) cc_final: 0.7750 (m-40) REVERT: A 168 TRP cc_start: 0.5885 (p90) cc_final: 0.5597 (p90) REVERT: A 200 MET cc_start: 0.6748 (tpt) cc_final: 0.6513 (tpt) REVERT: A 269 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 283 GLU cc_start: 0.8053 (pp20) cc_final: 0.7428 (pp20) REVERT: A 287 ASP cc_start: 0.7838 (m-30) cc_final: 0.7248 (m-30) REVERT: A 321 ILE cc_start: 0.8345 (pt) cc_final: 0.8063 (pt) REVERT: A 450 PHE cc_start: 0.7848 (m-10) cc_final: 0.7405 (m-10) REVERT: A 479 ARG cc_start: 0.7467 (ptt180) cc_final: 0.7186 (ptt180) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.1537 time to fit residues: 26.3137 Evaluate side-chains 127 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 269 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 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 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: 4.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.160972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.137631 restraints weight = 9390.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.141403 restraints weight = 5718.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144169 restraints weight = 3999.950| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4314 Z= 0.160 Angle : 0.693 7.942 5885 Z= 0.354 Chirality : 0.042 0.146 642 Planarity : 0.004 0.026 722 Dihedral : 6.022 43.062 599 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.76 % Allowed : 22.54 % Favored : 73.71 % 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: -0.70 (0.37), residues: 530 helix: 0.01 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.26 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.009 0.003 HIS A 347 PHE 0.021 0.002 PHE A 404 TYR 0.019 0.002 TYR A 139 ARG 0.002 0.000 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 256) hydrogen bonds : angle 5.32027 ( 750) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.70748 ( 2) covalent geometry : bond 0.00350 ( 4313) covalent geometry : angle 0.69288 ( 5883) *********************** 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 142 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8199 (m110) cc_final: 0.7828 (m-40) REVERT: A 168 TRP cc_start: 0.5949 (p90) cc_final: 0.5697 (p90) REVERT: A 269 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 283 GLU cc_start: 0.8156 (pp20) cc_final: 0.7472 (pp20) REVERT: A 287 ASP cc_start: 0.7928 (m-30) cc_final: 0.7310 (m-30) REVERT: A 321 ILE cc_start: 0.8344 (pt) cc_final: 0.8044 (pt) REVERT: A 450 PHE cc_start: 0.7947 (m-10) cc_final: 0.7541 (m-10) REVERT: A 462 PHE cc_start: 0.8482 (t80) cc_final: 0.8246 (t80) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.1368 time to fit residues: 23.3560 Evaluate side-chains 133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 269 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 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: 2.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 196 ASN ** A 565 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133081 restraints weight = 9306.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136624 restraints weight = 5602.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139041 restraints weight = 3900.220| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4314 Z= 0.223 Angle : 0.764 8.351 5885 Z= 0.395 Chirality : 0.045 0.220 642 Planarity : 0.005 0.035 722 Dihedral : 6.265 38.999 599 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.69 % Allowed : 23.47 % Favored : 71.83 % 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: -0.99 (0.37), residues: 530 helix: -0.29 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.22 (0.54), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 193 HIS 0.008 0.003 HIS A 347 PHE 0.019 0.002 PHE A 87 TYR 0.022 0.002 TYR A 139 ARG 0.004 0.001 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 256) hydrogen bonds : angle 5.53800 ( 750) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.07837 ( 2) covalent geometry : bond 0.00493 ( 4313) covalent geometry : angle 0.76433 ( 5883) *********************** 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 145 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8463 (m-40) cc_final: 0.8065 (m-40) REVERT: A 269 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7658 (mm) REVERT: A 283 GLU cc_start: 0.8314 (pp20) cc_final: 0.7637 (pp20) REVERT: A 287 ASP cc_start: 0.8073 (m-30) cc_final: 0.7366 (m-30) REVERT: A 321 ILE cc_start: 0.8333 (pt) cc_final: 0.7935 (pt) REVERT: A 487 MET cc_start: 0.7091 (tpp) cc_final: 0.6016 (tpp) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.1447 time to fit residues: 24.8158 Evaluate side-chains 134 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 269 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4157 r_free = 0.4157 target = 0.160195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.137834 restraints weight = 9294.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.141596 restraints weight = 5668.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144232 restraints weight = 3953.177| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4314 Z= 0.143 Angle : 0.697 8.059 5885 Z= 0.359 Chirality : 0.043 0.214 642 Planarity : 0.004 0.028 722 Dihedral : 5.973 37.906 599 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.99 % Allowed : 25.12 % 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: -0.77 (0.37), residues: 530 helix: -0.08 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.20 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.010 0.002 HIS A 347 PHE 0.017 0.002 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 256) hydrogen bonds : angle 5.39115 ( 750) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.75775 ( 2) covalent geometry : bond 0.00311 ( 4313) covalent geometry : angle 0.69727 ( 5883) *********************** 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 143 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8226 (m110) cc_final: 0.7932 (m-40) REVERT: A 269 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 283 GLU cc_start: 0.8167 (pp20) cc_final: 0.7550 (pp20) REVERT: A 287 ASP cc_start: 0.7887 (m-30) cc_final: 0.7378 (m-30) REVERT: A 321 ILE cc_start: 0.8296 (pt) cc_final: 0.7986 (pt) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.1498 time to fit residues: 26.5256 Evaluate side-chains 133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 269 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 45 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.160984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138145 restraints weight = 9195.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141814 restraints weight = 5699.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.144469 restraints weight = 4053.068| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4314 Z= 0.142 Angle : 0.729 9.302 5885 Z= 0.367 Chirality : 0.044 0.207 642 Planarity : 0.004 0.026 722 Dihedral : 5.905 37.708 599 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.52 % Allowed : 26.29 % Favored : 70.19 % 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: -0.64 (0.37), residues: 530 helix: 0.04 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.21 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.009 0.003 HIS A 347 PHE 0.021 0.002 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.002 0.000 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 256) hydrogen bonds : angle 5.34985 ( 750) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.67866 ( 2) covalent geometry : bond 0.00312 ( 4313) covalent geometry : angle 0.72867 ( 5883) *********************** 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 135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8160 (m110) cc_final: 0.7927 (m-40) REVERT: A 269 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 283 GLU cc_start: 0.8134 (pp20) cc_final: 0.7507 (pp20) REVERT: A 287 ASP cc_start: 0.7857 (m-30) cc_final: 0.7342 (m-30) REVERT: A 321 ILE cc_start: 0.8270 (pt) cc_final: 0.7995 (pt) REVERT: A 450 PHE cc_start: 0.7985 (m-10) cc_final: 0.7726 (m-10) REVERT: A 479 ARG cc_start: 0.7519 (ptt180) cc_final: 0.7233 (ptt180) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1445 time to fit residues: 24.0683 Evaluate side-chains 130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 269 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.167221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146070 restraints weight = 8493.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149845 restraints weight = 4871.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152463 restraints weight = 3268.735| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4314 Z= 0.137 Angle : 0.737 10.228 5885 Z= 0.369 Chirality : 0.043 0.201 642 Planarity : 0.004 0.025 722 Dihedral : 5.821 37.606 599 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.52 % Allowed : 25.35 % Favored : 71.13 % 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: -0.58 (0.37), residues: 530 helix: 0.12 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.009 0.002 HIS A 347 PHE 0.020 0.001 PHE A 385 TYR 0.027 0.002 TYR A 551 ARG 0.001 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 256) hydrogen bonds : angle 5.32547 ( 750) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.70648 ( 2) covalent geometry : bond 0.00299 ( 4313) covalent geometry : angle 0.73703 ( 5883) *********************** 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 134 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8101 (m110) cc_final: 0.7898 (m-40) REVERT: A 269 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7413 (mm) REVERT: A 283 GLU cc_start: 0.8068 (pp20) cc_final: 0.7487 (pp20) REVERT: A 287 ASP cc_start: 0.7847 (m-30) cc_final: 0.7342 (m-30) REVERT: A 321 ILE cc_start: 0.8233 (pt) cc_final: 0.7991 (pt) REVERT: A 391 MET cc_start: 0.7748 (mtt) cc_final: 0.7495 (mtt) REVERT: A 450 PHE cc_start: 0.7920 (m-10) cc_final: 0.7665 (m-10) REVERT: A 479 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7132 (ptt180) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.1654 time to fit residues: 27.4909 Evaluate side-chains 129 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 269 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 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: 0.6980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140439 restraints weight = 9323.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144259 restraints weight = 5705.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146980 restraints weight = 3981.949| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4314 Z= 0.140 Angle : 0.751 10.348 5885 Z= 0.376 Chirality : 0.043 0.197 642 Planarity : 0.004 0.024 722 Dihedral : 5.791 37.501 599 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.52 % Allowed : 26.06 % 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: -0.48 (0.37), residues: 530 helix: 0.17 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -1.12 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.008 0.002 HIS A 347 PHE 0.029 0.002 PHE A 447 TYR 0.022 0.001 TYR A 139 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 256) hydrogen bonds : angle 5.32219 ( 750) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.48196 ( 2) covalent geometry : bond 0.00308 ( 4313) covalent geometry : angle 0.75059 ( 5883) ********************** 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 137 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 283 GLU cc_start: 0.8141 (pp20) cc_final: 0.7617 (pp20) REVERT: A 287 ASP cc_start: 0.7816 (m-30) cc_final: 0.7333 (m-30) REVERT: A 321 ILE cc_start: 0.8215 (pt) cc_final: 0.7999 (pt) REVERT: A 391 MET cc_start: 0.7822 (mtt) cc_final: 0.7579 (mtt) REVERT: A 479 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7157 (ptt180) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1240 time to fit residues: 20.6220 Evaluate side-chains 133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 269 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 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 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141418 restraints weight = 9245.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145272 restraints weight = 5609.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.148043 restraints weight = 3905.064| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4314 Z= 0.144 Angle : 0.787 12.743 5885 Z= 0.393 Chirality : 0.044 0.242 642 Planarity : 0.004 0.024 722 Dihedral : 5.792 37.545 599 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.05 % Allowed : 27.93 % 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: -0.40 (0.37), residues: 530 helix: 0.22 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.07 (0.52), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 500 HIS 0.007 0.002 HIS A 347 PHE 0.030 0.002 PHE A 447 TYR 0.037 0.002 TYR A 551 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 256) hydrogen bonds : angle 5.31504 ( 750) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.50343 ( 2) covalent geometry : bond 0.00313 ( 4313) covalent geometry : angle 0.78749 ( 5883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2300.62 seconds wall clock time: 41 minutes 45.67 seconds (2505.67 seconds total)