Starting phenix.real_space_refine on Thu Mar 6 09:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekd_28199/03_2025/8ekd_28199.cif" } resolution = 3.6 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= 0.003 sd= 0.278 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3152 atoms to isotropic. 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 13 5.16 5 C 2075 2.51 5 N 540 2.21 5 O 611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3239 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 968 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 857 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1400 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.52, per 1000 atoms: 0.78 Number of scatterers: 3239 At special positions: 0 Unit cell: (94.462, 60.818, 80.228, 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 13 16.00 O 611 8.00 N 540 7.00 C 2075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " 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 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 353.8 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 6.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'E' and resid 64 through 67 Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 365 through 371 removed outlier: 3.907A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 416 through 421 removed outlier: 3.549A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.506A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 82 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.212A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.506A pdb=" N ASN F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.644A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.503A pdb=" N TYR G 396 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 398 " --> pdb=" O VAL G 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 452 through 454 71 hydrogen bonds defined for protein. 189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 893 1.33 - 1.45: 677 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.81: 17 Bond restraints: 3323 Sorted by residual: bond pdb=" N GLN G 474 " pdb=" CA GLN G 474 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.22e-02 6.72e+03 7.66e+00 bond pdb=" CB PRO G 507 " pdb=" CG PRO G 507 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.65e+00 bond pdb=" CA SER G 459 " pdb=" CB SER G 459 " ideal model delta sigma weight residual 1.527 1.487 0.040 1.44e-02 4.82e+03 7.58e+00 bond pdb=" N LYS G 458 " pdb=" CA LYS G 458 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.31e-02 5.83e+03 5.91e+00 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 4357 2.23 - 4.46: 121 4.46 - 6.69: 19 6.69 - 8.91: 7 8.91 - 11.14: 2 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N GLN G 474 " pdb=" CA GLN G 474 " pdb=" C GLN G 474 " ideal model delta sigma weight residual 110.28 121.42 -11.14 1.48e+00 4.57e-01 5.67e+01 angle pdb=" CA PRO G 507 " pdb=" N PRO G 507 " pdb=" CD PRO G 507 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 angle pdb=" C THR G 470 " pdb=" CA THR G 470 " pdb=" CB THR G 470 " ideal model delta sigma weight residual 111.22 103.83 7.39 1.23e+00 6.61e-01 3.61e+01 angle pdb=" CA ALA G 475 " pdb=" C ALA G 475 " pdb=" N GLY G 476 " ideal model delta sigma weight residual 119.63 114.99 4.64 8.10e-01 1.52e+00 3.28e+01 angle pdb=" C SER G 459 " pdb=" N ASN G 460 " pdb=" CA ASN G 460 " ideal model delta sigma weight residual 120.82 112.85 7.97 1.41e+00 5.03e-01 3.19e+01 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1670 21.36 - 42.72: 236 42.72 - 64.07: 26 64.07 - 85.43: 9 85.43 - 106.79: 8 Dihedral angle restraints: 1949 sinusoidal: 769 harmonic: 1180 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual 93.00 44.64 48.36 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CA PRO F 65 " pdb=" C PRO F 65 " pdb=" N ASP F 66 " pdb=" CA ASP F 66 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C2 NAG G 601 " pdb=" C3 NAG G 601 " pdb=" C4 NAG G 601 " pdb=" O4 NAG G 601 " ideal model delta sinusoidal sigma weight residual 175.11 68.32 106.79 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 1946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 356 0.045 - 0.091: 83 0.091 - 0.136: 25 0.136 - 0.182: 3 0.182 - 0.227: 6 Chirality restraints: 473 Sorted by residual: chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR G 470 " pdb=" N THR G 470 " pdb=" C THR G 470 " pdb=" CB THR G 470 " both_signs ideal model delta sigma weight residual False 2.53 2.75 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG G 457 " pdb=" N ARG G 457 " pdb=" C ARG G 457 " pdb=" CB ARG G 457 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 470 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 383 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 384 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 384 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO G 384 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 48 " -0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO F 49 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 471 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLU G 471 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU G 471 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE G 472 " -0.019 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 256 2.73 - 3.27: 3328 3.27 - 3.82: 5704 3.82 - 4.36: 6739 4.36 - 4.90: 11108 Nonbonded interactions: 27135 Sorted by model distance: nonbonded pdb=" O PRO F 8 " pdb=" OG1 THR F 107 " model vdw 2.190 3.040 nonbonded pdb=" O PRO G 479 " pdb=" SG CYS G 480 " model vdw 2.195 3.400 nonbonded pdb=" OH TYR E 106 " pdb=" O TYR F 97 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU G 406 " pdb=" NE2 GLN G 409 " model vdw 2.205 3.120 nonbonded pdb=" O GLY E 116 " pdb=" OG SER F 62 " model vdw 2.239 3.040 ... (remaining 27130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 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 0.138 3323 Z= 0.334 Angle : 0.883 11.143 4506 Z= 0.531 Chirality : 0.049 0.227 473 Planarity : 0.009 0.117 580 Dihedral : 19.664 106.791 1196 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.77 % Allowed : 38.94 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.67 (0.40), residues: 399 helix: -0.53 (1.97), residues: 7 sheet: -1.25 (0.46), residues: 120 loop : -1.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 121 HIS 0.002 0.001 HIS G 505 PHE 0.008 0.001 PHE E 118 TYR 0.017 0.002 TYR E 105 ARG 0.009 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.5854 (pm20) cc_final: 0.5353 (pm20) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.1777 time to fit residues: 21.0296 Evaluate side-chains 102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain G residue 457 ARG Chi-restraints excluded: chain G residue 459 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160798 restraints weight = 4076.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166017 restraints weight = 2121.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169537 restraints weight = 1404.283| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3323 Z= 0.208 Angle : 0.667 7.060 4506 Z= 0.342 Chirality : 0.045 0.225 473 Planarity : 0.007 0.075 580 Dihedral : 8.686 57.222 489 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.60 % Allowed : 30.38 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.40), residues: 399 helix: -0.53 (1.96), residues: 7 sheet: -1.17 (0.51), residues: 102 loop : -1.04 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.008 0.001 PHE G 497 TYR 0.014 0.002 TYR E 105 ARG 0.003 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4356 (OUTLIER) cc_final: 0.3308 (m-80) REVERT: E 112 GLU cc_start: 0.5510 (pm20) cc_final: 0.5123 (pm20) REVERT: F 67 ARG cc_start: 0.5730 (ptt-90) cc_final: 0.5166 (ptt-90) REVERT: G 357 ARG cc_start: 0.7532 (tmt170) cc_final: 0.7289 (tmm-80) REVERT: G 406 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: G 429 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7196 (p90) REVERT: G 459 SER cc_start: 0.8413 (t) cc_final: 0.7762 (p) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.1566 time to fit residues: 20.4726 Evaluate side-chains 106 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 429 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145718 restraints weight = 4213.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150352 restraints weight = 2297.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153423 restraints weight = 1574.800| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3323 Z= 0.393 Angle : 0.724 6.490 4506 Z= 0.374 Chirality : 0.047 0.270 473 Planarity : 0.006 0.061 580 Dihedral : 6.416 52.318 476 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.96 % Allowed : 30.68 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.51 (0.40), residues: 399 helix: -0.22 (2.01), residues: 7 sheet: -0.96 (0.49), residues: 110 loop : -1.07 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 121 HIS 0.001 0.001 HIS G 505 PHE 0.027 0.002 PHE E 118 TYR 0.017 0.002 TYR F 42 ARG 0.004 0.001 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4731 (OUTLIER) cc_final: 0.3764 (m-80) REVERT: E 112 GLU cc_start: 0.5745 (pm20) cc_final: 0.5307 (pm20) REVERT: F 67 ARG cc_start: 0.6064 (ptt-90) cc_final: 0.5600 (ptt-90) REVERT: G 357 ARG cc_start: 0.7568 (tmt170) cc_final: 0.7355 (tmm-80) REVERT: G 398 ASP cc_start: 0.8140 (m-30) cc_final: 0.7210 (m-30) REVERT: G 406 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: G 409 GLN cc_start: 0.7061 (mt0) cc_final: 0.6487 (tt0) REVERT: G 429 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6828 (p90) REVERT: G 459 SER cc_start: 0.8339 (t) cc_final: 0.7940 (p) outliers start: 27 outliers final: 13 residues processed: 119 average time/residue: 0.1812 time to fit residues: 25.4880 Evaluate side-chains 114 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 473 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.0040 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4038 r_free = 0.4038 target = 0.179152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150811 restraints weight = 4186.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155607 restraints weight = 2221.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158783 restraints weight = 1487.315| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3323 Z= 0.250 Angle : 0.671 7.250 4506 Z= 0.343 Chirality : 0.044 0.198 473 Planarity : 0.006 0.058 580 Dihedral : 5.778 40.471 476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 8.85 % Allowed : 28.91 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.41 (0.41), residues: 399 helix: -0.23 (1.93), residues: 7 sheet: -0.76 (0.50), residues: 115 loop : -1.06 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.021 0.002 PHE E 118 TYR 0.013 0.002 TYR E 105 ARG 0.003 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.3559 (m-80) REVERT: F 67 ARG cc_start: 0.6155 (ptt-90) cc_final: 0.5781 (ptt-90) REVERT: G 357 ARG cc_start: 0.7521 (tmt170) cc_final: 0.7225 (tmm-80) REVERT: G 396 TYR cc_start: 0.6700 (m-10) cc_final: 0.6393 (m-10) REVERT: G 398 ASP cc_start: 0.8173 (m-30) cc_final: 0.7404 (m-30) REVERT: G 406 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: G 409 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: G 429 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6892 (p90) REVERT: G 495 TYR cc_start: 0.4557 (OUTLIER) cc_final: 0.3953 (m-80) outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.1597 time to fit residues: 22.9958 Evaluate side-chains 119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 GLN ** F 96 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.184189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155021 restraints weight = 4108.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.160060 restraints weight = 2180.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163265 restraints weight = 1470.765| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3323 Z= 0.245 Angle : 0.670 8.180 4506 Z= 0.341 Chirality : 0.044 0.221 473 Planarity : 0.006 0.059 580 Dihedral : 5.527 35.376 476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 8.55 % Allowed : 30.38 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.37 (0.41), residues: 399 helix: -0.35 (1.86), residues: 7 sheet: -0.70 (0.50), residues: 115 loop : -1.04 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.019 0.001 PHE E 118 TYR 0.014 0.002 TYR E 106 ARG 0.003 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.3525 (m-80) REVERT: F 59 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6631 (tm-30) REVERT: F 67 ARG cc_start: 0.6145 (ptt-90) cc_final: 0.5753 (ptt-90) REVERT: G 357 ARG cc_start: 0.7553 (tmt170) cc_final: 0.7318 (tmm-80) REVERT: G 398 ASP cc_start: 0.8135 (m-30) cc_final: 0.7585 (m-30) REVERT: G 406 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: G 409 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: G 429 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6806 (p90) REVERT: G 495 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.3964 (m-80) REVERT: G 501 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5999 (m-10) outliers start: 29 outliers final: 15 residues processed: 121 average time/residue: 0.1769 time to fit residues: 25.2730 Evaluate side-chains 119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4030 r_free = 0.4030 target = 0.177096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147199 restraints weight = 4238.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152064 restraints weight = 2273.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155151 restraints weight = 1537.146| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3323 Z= 0.396 Angle : 0.759 8.973 4506 Z= 0.386 Chirality : 0.047 0.262 473 Planarity : 0.007 0.063 580 Dihedral : 5.887 34.949 476 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 9.44 % Allowed : 29.20 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.50 (0.41), residues: 399 helix: -0.07 (1.98), residues: 7 sheet: -0.75 (0.49), residues: 115 loop : -1.17 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.018 0.002 PHE E 118 TYR 0.017 0.003 TYR G 380 ARG 0.003 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4642 (OUTLIER) cc_final: 0.3718 (m-80) REVERT: F 60 ARG cc_start: 0.6118 (ttm-80) cc_final: 0.5682 (tpp80) REVERT: G 357 ARG cc_start: 0.7638 (tmt170) cc_final: 0.7343 (tmm-80) REVERT: G 371 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.5636 (p90) REVERT: G 398 ASP cc_start: 0.8213 (m-30) cc_final: 0.7357 (m-30) REVERT: G 406 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: G 409 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6511 (tt0) REVERT: G 429 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6681 (p90) REVERT: G 495 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.4028 (m-80) REVERT: G 501 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6167 (m-10) outliers start: 32 outliers final: 17 residues processed: 125 average time/residue: 0.1717 time to fit residues: 25.5246 Evaluate side-chains 124 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 GLN ** F 96 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.182673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152907 restraints weight = 4157.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157787 restraints weight = 2201.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160949 restraints weight = 1498.102| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 : 0.004 0.025 3323 Z= 0.252 Angle : 0.701 9.058 4506 Z= 0.352 Chirality : 0.044 0.217 473 Planarity : 0.006 0.062 580 Dihedral : 5.630 32.674 476 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 8.55 % Allowed : 29.50 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.42 (0.41), residues: 399 helix: -0.10 (2.02), residues: 7 sheet: -0.69 (0.49), residues: 115 loop : -1.11 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.015 0.001 PHE E 118 TYR 0.015 0.002 TYR G 473 ARG 0.003 0.000 ARG G 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4481 (OUTLIER) cc_final: 0.3551 (m-80) REVERT: F 60 ARG cc_start: 0.6090 (ttm-80) cc_final: 0.5658 (tpp80) REVERT: G 357 ARG cc_start: 0.7554 (tmt170) cc_final: 0.7232 (tmm-80) REVERT: G 371 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5582 (p90) REVERT: G 398 ASP cc_start: 0.8215 (m-30) cc_final: 0.7602 (m-30) REVERT: G 406 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: G 409 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: G 429 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6649 (p90) REVERT: G 495 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.3983 (m-80) REVERT: G 501 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6072 (m-10) outliers start: 29 outliers final: 17 residues processed: 123 average time/residue: 0.1632 time to fit residues: 23.6733 Evaluate side-chains 125 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151476 restraints weight = 4131.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156387 restraints weight = 2219.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159746 restraints weight = 1522.814| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3323 Z= 0.293 Angle : 0.729 9.424 4506 Z= 0.365 Chirality : 0.045 0.244 473 Planarity : 0.006 0.064 580 Dihedral : 5.653 31.638 476 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 9.14 % Allowed : 30.68 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.46 (0.41), residues: 399 helix: 0.11 (2.12), residues: 7 sheet: -0.73 (0.48), residues: 115 loop : -1.14 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.016 0.002 PHE E 118 TYR 0.016 0.002 TYR G 449 ARG 0.003 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.3641 (m-80) REVERT: F 36 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6769 (ptmt) REVERT: F 60 ARG cc_start: 0.6021 (ttm-80) cc_final: 0.5720 (tpp80) REVERT: G 356 LYS cc_start: 0.8269 (mptt) cc_final: 0.8001 (mptt) REVERT: G 357 ARG cc_start: 0.7587 (tmt170) cc_final: 0.7253 (tmm-80) REVERT: G 371 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5575 (p90) REVERT: G 398 ASP cc_start: 0.8207 (m-30) cc_final: 0.7590 (m-30) REVERT: G 406 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: G 409 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: G 429 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6620 (p90) REVERT: G 495 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.3935 (m-80) REVERT: G 501 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6100 (m-10) outliers start: 31 outliers final: 19 residues processed: 121 average time/residue: 0.1769 time to fit residues: 25.2502 Evaluate side-chains 128 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4102 r_free = 0.4102 target = 0.185373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155663 restraints weight = 4124.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160688 restraints weight = 2160.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163701 restraints weight = 1455.179| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3323 Z= 0.248 Angle : 0.717 9.657 4506 Z= 0.357 Chirality : 0.044 0.238 473 Planarity : 0.006 0.065 580 Dihedral : 5.468 29.863 476 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 8.55 % Allowed : 31.27 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.42 (0.41), residues: 399 helix: 0.05 (2.10), residues: 7 sheet: -0.67 (0.48), residues: 115 loop : -1.13 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.016 0.001 PHE E 118 TYR 0.011 0.002 TYR E 105 ARG 0.002 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4509 (OUTLIER) cc_final: 0.3577 (m-80) REVERT: F 60 ARG cc_start: 0.6096 (ttm-80) cc_final: 0.5751 (tpp80) REVERT: G 357 ARG cc_start: 0.7549 (tmt170) cc_final: 0.7282 (tmm-80) REVERT: G 371 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5563 (p90) REVERT: G 398 ASP cc_start: 0.8152 (m-30) cc_final: 0.7550 (m-30) REVERT: G 406 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: G 409 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6508 (tt0) REVERT: G 429 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6497 (p90) REVERT: G 495 TYR cc_start: 0.4493 (OUTLIER) cc_final: 0.3986 (m-80) REVERT: G 501 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.6082 (m-10) outliers start: 29 outliers final: 19 residues processed: 119 average time/residue: 0.1740 time to fit residues: 24.4934 Evaluate side-chains 121 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.186272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156567 restraints weight = 4060.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161575 restraints weight = 2165.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164897 restraints weight = 1468.236| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3323 Z= 0.243 Angle : 0.730 10.157 4506 Z= 0.362 Chirality : 0.044 0.251 473 Planarity : 0.006 0.066 580 Dihedral : 5.332 27.597 476 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 8.85 % Allowed : 30.68 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.43 (0.41), residues: 399 helix: 0.07 (2.09), residues: 7 sheet: -0.70 (0.48), residues: 115 loop : -1.12 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.016 0.002 PHE E 118 TYR 0.014 0.002 TYR G 449 ARG 0.002 0.000 ARG F 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.3642 (m-80) REVERT: F 7 SER cc_start: 0.8233 (t) cc_final: 0.7999 (t) REVERT: F 20 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7200 (p) REVERT: F 60 ARG cc_start: 0.6107 (ttm-80) cc_final: 0.5849 (tpp80) REVERT: G 357 ARG cc_start: 0.7510 (tmt170) cc_final: 0.7172 (tmm-80) REVERT: G 371 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5540 (p90) REVERT: G 398 ASP cc_start: 0.8178 (m-30) cc_final: 0.7581 (m-30) REVERT: G 406 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: G 409 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: G 429 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6591 (p90) REVERT: G 495 TYR cc_start: 0.4505 (OUTLIER) cc_final: 0.4040 (m-80) REVERT: G 501 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6061 (m-10) outliers start: 30 outliers final: 19 residues processed: 117 average time/residue: 0.1768 time to fit residues: 24.3904 Evaluate side-chains 122 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.187285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157463 restraints weight = 4047.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162613 restraints weight = 2149.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165679 restraints weight = 1447.309| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.227 Angle : 0.750 10.368 4506 Z= 0.366 Chirality : 0.044 0.248 473 Planarity : 0.006 0.066 580 Dihedral : 5.218 25.435 476 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 7.96 % Allowed : 31.86 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.42 (0.41), residues: 399 helix: 0.06 (2.08), residues: 7 sheet: -0.65 (0.48), residues: 115 loop : -1.13 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.013 0.001 PHE E 118 TYR 0.013 0.002 TYR G 449 ARG 0.003 0.000 ARG F 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.24 seconds wall clock time: 26 minutes 52.65 seconds (1612.65 seconds total)