Starting phenix.real_space_refine on Sat Apr 26 18:50:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.map" model { file = "/net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv9_38693/04_2025/8xv9_38693.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 17 5.16 5 C 2127 2.51 5 N 472 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3110 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.89 Number of scatterers: 3147 At special positions: 0 Unit cell: (67.41, 70.62, 77.04, 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 17 16.00 O 531 8.00 N 472 7.00 C 2127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.79 Conformation dependent library (CDL) restraints added in 375.5 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.765A pdb=" N TYR A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.915A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.705A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.833A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 removed outlier: 3.829A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.586A pdb=" N SER A 129 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.087A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 307 removed outlier: 5.277A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 335 Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.616A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.513A pdb=" N CYS A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.848A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 459 removed outlier: 3.574A pdb=" N GLN A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 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: 0.77 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 891 1.35 - 1.47: 974 1.47 - 1.59: 1351 1.59 - 1.72: 0 1.72 - 1.84: 30 Bond restraints: 3246 Sorted by residual: bond pdb=" CAQ 2TA A 501 " pdb=" CAR 2TA A 501 " ideal model delta sigma weight residual 1.526 1.343 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" CAT 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.456 1.285 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" CAQ 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.454 1.583 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NBE 2TA A 501 " pdb=" SBD 2TA A 501 " ideal model delta sigma weight residual 1.639 1.757 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " ideal model delta sigma weight residual 1.361 1.475 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 3241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 4380 3.38 - 6.76: 41 6.76 - 10.14: 14 10.14 - 13.52: 1 13.52 - 16.90: 1 Bond angle restraints: 4437 Sorted by residual: angle pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" CAG 2TA A 501 " ideal model delta sigma weight residual 131.32 114.42 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C4 2TA A 501 " pdb=" NAW 2TA A 501 " pdb=" CAX 2TA A 501 " ideal model delta sigma weight residual 131.24 120.10 11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ILE A 36 " pdb=" C ILE A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 118.88 123.77 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" OBJ 2TA A 501 " pdb=" SBD 2TA A 501 " pdb=" OBK 2TA A 501 " ideal model delta sigma weight residual 118.13 109.12 9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" N TYR A 14 " pdb=" CA TYR A 14 " pdb=" C TYR A 14 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.71e+00 ... (remaining 4432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 1801 28.97 - 57.95: 22 57.95 - 86.92: 7 86.92 - 115.90: 2 115.90 - 144.87: 1 Dihedral angle restraints: 1833 sinusoidal: 681 harmonic: 1152 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CAG 2TA A 501 " pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sinusoidal sigma weight residual -0.72 -145.59 144.87 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 292 0.035 - 0.071: 148 0.071 - 0.106: 45 0.106 - 0.141: 13 0.141 - 0.176: 4 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TYR A 14 " pdb=" N TYR A 14 " pdb=" C TYR A 14 " pdb=" CB TYR A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 499 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.018 2.00e-02 2.50e+03 1.64e-02 5.38e+00 pdb=" CG TYR A 373 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 29 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 30 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 61 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TYR A 61 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 61 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1181 2.90 - 3.40: 3062 3.40 - 3.90: 5208 3.90 - 4.40: 5520 4.40 - 4.90: 9624 Nonbonded interactions: 24595 Sorted by model distance: nonbonded pdb=" OE1 GLU A 32 " pdb=" NAW 2TA A 501 " model vdw 2.402 3.120 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.412 3.040 nonbonded pdb=" O PHE A 22 " pdb=" OG SER A 26 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.476 3.040 nonbonded pdb=" O LYS A 270 " pdb=" OG SER A 274 " model vdw 2.485 3.040 ... (remaining 24590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 : 0.008 0.183 3246 Z= 0.409 Angle : 0.936 16.896 4437 Z= 0.449 Chirality : 0.047 0.176 502 Planarity : 0.007 0.051 529 Dihedral : 12.311 144.871 1097 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -3.53 (0.31), residues: 384 helix: -1.68 (0.22), residues: 279 sheet: None (None), residues: 0 loop : -3.83 (0.44), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 59 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.041 0.002 TYR A 373 ARG 0.001 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.10817 ( 220) hydrogen bonds : angle 5.77522 ( 654) covalent geometry : bond 0.00808 ( 3246) covalent geometry : angle 0.93620 ( 4437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.7605 (p) cc_final: 0.7084 (m) REVERT: A 36 ILE cc_start: 0.7864 (tp) cc_final: 0.7439 (tp) REVERT: A 77 VAL cc_start: 0.7653 (m) cc_final: 0.7315 (t) REVERT: A 115 MET cc_start: 0.6896 (ttp) cc_final: 0.6562 (ttp) REVERT: A 152 THR cc_start: 0.7629 (m) cc_final: 0.7115 (p) REVERT: A 306 LYS cc_start: 0.6487 (mmtt) cc_final: 0.6262 (mmtt) REVERT: A 364 HIS cc_start: 0.6529 (t70) cc_final: 0.6234 (t-90) REVERT: A 369 ILE cc_start: 0.8050 (tp) cc_final: 0.7687 (tp) REVERT: A 389 ILE cc_start: 0.7768 (mt) cc_final: 0.7465 (mt) REVERT: A 423 VAL cc_start: 0.7605 (t) cc_final: 0.7056 (m) REVERT: A 440 LEU cc_start: 0.7185 (tp) cc_final: 0.6565 (mt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1252 time to fit residues: 15.6948 Evaluate side-chains 79 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 294 GLN A 356 ASN A 364 HIS ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140888 restraints weight = 5626.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145018 restraints weight = 3003.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147711 restraints weight = 1846.316| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3246 Z= 0.187 Angle : 0.661 6.252 4437 Z= 0.343 Chirality : 0.043 0.157 502 Planarity : 0.005 0.042 529 Dihedral : 13.701 155.494 440 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.60 % Allowed : 11.71 % Favored : 87.69 % 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: -0.57 (0.41), residues: 384 helix: 0.47 (0.29), residues: 284 sheet: None (None), residues: 0 loop : -2.78 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.026 0.002 PHE A 439 TYR 0.029 0.002 TYR A 126 ARG 0.001 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 220) hydrogen bonds : angle 4.05596 ( 654) covalent geometry : bond 0.00391 ( 3246) covalent geometry : angle 0.66133 ( 4437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7583 (tp) REVERT: A 77 VAL cc_start: 0.7701 (m) cc_final: 0.7471 (t) REVERT: A 152 THR cc_start: 0.7778 (m) cc_final: 0.7109 (p) REVERT: A 156 VAL cc_start: 0.7968 (t) cc_final: 0.7696 (p) REVERT: A 167 MET cc_start: 0.6195 (mmm) cc_final: 0.5746 (ptp) REVERT: A 301 ILE cc_start: 0.7742 (mt) cc_final: 0.7534 (mt) REVERT: A 366 THR cc_start: 0.8162 (p) cc_final: 0.7881 (p) REVERT: A 369 ILE cc_start: 0.7828 (tp) cc_final: 0.7601 (tp) REVERT: A 386 LEU cc_start: 0.7995 (mt) cc_final: 0.7774 (mm) REVERT: A 423 VAL cc_start: 0.7712 (t) cc_final: 0.7262 (m) outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1239 time to fit residues: 14.5095 Evaluate side-chains 88 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138909 restraints weight = 5509.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142980 restraints weight = 2981.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145753 restraints weight = 1840.498| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3246 Z= 0.199 Angle : 0.645 5.737 4437 Z= 0.343 Chirality : 0.043 0.154 502 Planarity : 0.005 0.043 529 Dihedral : 13.958 158.415 440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.40 % Allowed : 13.81 % Favored : 83.78 % 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: 0.03 (0.42), residues: 384 helix: 0.92 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -2.81 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 12 HIS 0.003 0.001 HIS A 364 PHE 0.018 0.002 PHE A 439 TYR 0.029 0.002 TYR A 445 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 220) hydrogen bonds : angle 3.97231 ( 654) covalent geometry : bond 0.00417 ( 3246) covalent geometry : angle 0.64543 ( 4437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7885 (mmm) cc_final: 0.7389 (mpp) REVERT: A 91 ILE cc_start: 0.7754 (mt) cc_final: 0.7403 (mm) REVERT: A 128 TYR cc_start: 0.6769 (m-80) cc_final: 0.6444 (m-80) REVERT: A 152 THR cc_start: 0.8033 (m) cc_final: 0.7361 (p) REVERT: A 156 VAL cc_start: 0.7987 (t) cc_final: 0.7711 (p) REVERT: A 298 TYR cc_start: 0.7263 (m-10) cc_final: 0.6652 (m-10) REVERT: A 363 MET cc_start: 0.6435 (tpt) cc_final: 0.6167 (mtt) REVERT: A 364 HIS cc_start: 0.6705 (t-90) cc_final: 0.6452 (t-90) REVERT: A 421 MET cc_start: 0.7548 (ttp) cc_final: 0.7323 (ttp) REVERT: A 423 VAL cc_start: 0.7950 (t) cc_final: 0.7512 (m) REVERT: A 440 LEU cc_start: 0.7263 (tp) cc_final: 0.6697 (mt) outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.1210 time to fit residues: 15.5320 Evaluate side-chains 93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A 438 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 = 0.4005 r_free = 0.4005 target = 0.156030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140444 restraints weight = 5489.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144484 restraints weight = 2977.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147175 restraints weight = 1829.045| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3246 Z= 0.153 Angle : 0.643 6.359 4437 Z= 0.331 Chirality : 0.041 0.153 502 Planarity : 0.005 0.066 529 Dihedral : 13.927 157.961 440 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.70 % Allowed : 16.82 % Favored : 80.48 % 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: 0.49 (0.42), residues: 384 helix: 1.19 (0.29), residues: 294 sheet: None (None), residues: 0 loop : -2.62 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.027 0.002 TYR A 126 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 220) hydrogen bonds : angle 3.86205 ( 654) covalent geometry : bond 0.00329 ( 3246) covalent geometry : angle 0.64304 ( 4437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7894 (mmm) cc_final: 0.7595 (mmm) REVERT: A 128 TYR cc_start: 0.6840 (m-80) cc_final: 0.6419 (m-80) REVERT: A 152 THR cc_start: 0.7920 (m) cc_final: 0.7279 (p) REVERT: A 156 VAL cc_start: 0.7948 (t) cc_final: 0.7661 (p) REVERT: A 366 THR cc_start: 0.8191 (p) cc_final: 0.7972 (p) REVERT: A 423 VAL cc_start: 0.7953 (t) cc_final: 0.7533 (m) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1043 time to fit residues: 12.7722 Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.0980 chunk 15 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142973 restraints weight = 5475.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147013 restraints weight = 2928.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.149834 restraints weight = 1798.051| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3246 Z= 0.119 Angle : 0.610 6.349 4437 Z= 0.306 Chirality : 0.040 0.137 502 Planarity : 0.004 0.054 529 Dihedral : 13.474 155.111 440 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.10 % Allowed : 19.52 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.43), residues: 384 helix: 1.68 (0.29), residues: 295 sheet: None (None), residues: 0 loop : -2.20 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.008 0.001 PHE A 325 TYR 0.023 0.002 TYR A 126 ARG 0.001 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 220) hydrogen bonds : angle 3.68690 ( 654) covalent geometry : bond 0.00241 ( 3246) covalent geometry : angle 0.60958 ( 4437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7830 (mmm) cc_final: 0.7535 (mmm) REVERT: A 36 ILE cc_start: 0.7983 (tp) cc_final: 0.7742 (tp) REVERT: A 148 LEU cc_start: 0.8007 (mt) cc_final: 0.7746 (mm) REVERT: A 152 THR cc_start: 0.7972 (m) cc_final: 0.7303 (p) REVERT: A 156 VAL cc_start: 0.7922 (t) cc_final: 0.7661 (p) REVERT: A 384 MET cc_start: 0.6718 (tpp) cc_final: 0.6456 (mpp) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.1225 time to fit residues: 13.8904 Evaluate side-chains 89 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139279 restraints weight = 5535.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143393 restraints weight = 3009.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146132 restraints weight = 1866.053| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3246 Z= 0.187 Angle : 0.682 6.269 4437 Z= 0.350 Chirality : 0.042 0.143 502 Planarity : 0.005 0.048 529 Dihedral : 13.686 156.267 440 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.00 % Allowed : 19.22 % Favored : 77.78 % 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: 0.92 (0.43), residues: 384 helix: 1.34 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.04 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 12 HIS 0.006 0.002 HIS A 364 PHE 0.017 0.002 PHE A 266 TYR 0.021 0.002 TYR A 445 ARG 0.002 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 220) hydrogen bonds : angle 3.95956 ( 654) covalent geometry : bond 0.00400 ( 3246) covalent geometry : angle 0.68158 ( 4437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7997 (mmm) cc_final: 0.7694 (mmm) REVERT: A 128 TYR cc_start: 0.6891 (m-80) cc_final: 0.6593 (m-80) REVERT: A 148 LEU cc_start: 0.8026 (mt) cc_final: 0.7822 (mm) REVERT: A 152 THR cc_start: 0.7942 (m) cc_final: 0.7284 (p) REVERT: A 156 VAL cc_start: 0.7962 (t) cc_final: 0.7713 (p) REVERT: A 167 MET cc_start: 0.6623 (mmm) cc_final: 0.6346 (ptp) REVERT: A 423 VAL cc_start: 0.7956 (t) cc_final: 0.7553 (m) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1063 time to fit residues: 12.4924 Evaluate side-chains 94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138338 restraints weight = 5358.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142376 restraints weight = 2927.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145096 restraints weight = 1818.637| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3246 Z= 0.195 Angle : 0.685 7.562 4437 Z= 0.352 Chirality : 0.042 0.136 502 Planarity : 0.004 0.046 529 Dihedral : 13.770 155.649 440 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.30 % Allowed : 20.12 % Favored : 76.58 % 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: 0.83 (0.43), residues: 384 helix: 1.27 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.05 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.018 0.002 PHE A 266 TYR 0.023 0.002 TYR A 445 ARG 0.002 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 220) hydrogen bonds : angle 3.97920 ( 654) covalent geometry : bond 0.00414 ( 3246) covalent geometry : angle 0.68450 ( 4437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.7988 (mmm) cc_final: 0.7535 (mmm) REVERT: A 128 TYR cc_start: 0.6949 (m-80) cc_final: 0.6628 (m-80) REVERT: A 152 THR cc_start: 0.7932 (m) cc_final: 0.7450 (p) REVERT: A 298 TYR cc_start: 0.7091 (m-10) cc_final: 0.6713 (m-10) REVERT: A 391 VAL cc_start: 0.8537 (t) cc_final: 0.8307 (p) REVERT: A 423 VAL cc_start: 0.7984 (t) cc_final: 0.7566 (m) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.1026 time to fit residues: 13.2861 Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139411 restraints weight = 5390.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143597 restraints weight = 2955.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.146421 restraints weight = 1826.272| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3246 Z= 0.157 Angle : 0.687 8.013 4437 Z= 0.342 Chirality : 0.041 0.130 502 Planarity : 0.004 0.044 529 Dihedral : 13.632 152.330 440 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.80 % Allowed : 21.92 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.43), residues: 384 helix: 1.55 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -1.89 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.007 0.002 HIS A 364 PHE 0.013 0.001 PHE A 266 TYR 0.024 0.002 TYR A 445 ARG 0.001 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 220) hydrogen bonds : angle 3.89718 ( 654) covalent geometry : bond 0.00340 ( 3246) covalent geometry : angle 0.68651 ( 4437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7935 (mmm) cc_final: 0.7486 (mmm) REVERT: A 128 TYR cc_start: 0.6910 (m-80) cc_final: 0.6622 (m-80) REVERT: A 152 THR cc_start: 0.7961 (m) cc_final: 0.7471 (p) REVERT: A 386 LEU cc_start: 0.7792 (mm) cc_final: 0.7305 (tt) REVERT: A 391 VAL cc_start: 0.8530 (t) cc_final: 0.8292 (p) REVERT: A 423 VAL cc_start: 0.7941 (t) cc_final: 0.7544 (m) outliers start: 6 outliers final: 6 residues processed: 91 average time/residue: 0.1033 time to fit residues: 12.4679 Evaluate side-chains 93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 29 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140262 restraints weight = 5449.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144584 restraints weight = 2954.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147270 restraints weight = 1810.564| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3246 Z= 0.161 Angle : 0.690 8.519 4437 Z= 0.344 Chirality : 0.040 0.133 502 Planarity : 0.004 0.038 529 Dihedral : 13.504 150.716 440 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.10 % Allowed : 22.82 % Favored : 75.08 % 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: 1.29 (0.44), residues: 384 helix: 1.59 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -1.83 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.013 0.001 PHE A 266 TYR 0.024 0.002 TYR A 445 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 220) hydrogen bonds : angle 3.89308 ( 654) covalent geometry : bond 0.00345 ( 3246) covalent geometry : angle 0.69020 ( 4437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7972 (mmm) cc_final: 0.7521 (mmm) REVERT: A 124 TYR cc_start: 0.7064 (m-80) cc_final: 0.6610 (t80) REVERT: A 128 TYR cc_start: 0.6976 (m-80) cc_final: 0.6650 (m-80) REVERT: A 152 THR cc_start: 0.7982 (m) cc_final: 0.7493 (p) REVERT: A 386 LEU cc_start: 0.7809 (mm) cc_final: 0.7286 (tt) REVERT: A 391 VAL cc_start: 0.8527 (t) cc_final: 0.8285 (p) REVERT: A 423 VAL cc_start: 0.7965 (t) cc_final: 0.7546 (m) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.1037 time to fit residues: 12.5493 Evaluate side-chains 94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 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 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138553 restraints weight = 5358.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142640 restraints weight = 2911.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145429 restraints weight = 1805.195| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3246 Z= 0.218 Angle : 0.738 8.735 4437 Z= 0.375 Chirality : 0.044 0.202 502 Planarity : 0.004 0.035 529 Dihedral : 13.615 150.803 440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.50 % Allowed : 23.42 % Favored : 75.08 % 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: 0.93 (0.43), residues: 384 helix: 1.29 (0.29), residues: 302 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.020 0.002 PHE A 266 TYR 0.024 0.002 TYR A 445 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 220) hydrogen bonds : angle 4.10358 ( 654) covalent geometry : bond 0.00467 ( 3246) covalent geometry : angle 0.73823 ( 4437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8002 (mmm) cc_final: 0.7562 (mmm) REVERT: A 128 TYR cc_start: 0.7131 (m-80) cc_final: 0.6806 (m-80) REVERT: A 152 THR cc_start: 0.8155 (m) cc_final: 0.7716 (p) REVERT: A 386 LEU cc_start: 0.7799 (mm) cc_final: 0.7313 (tt) REVERT: A 391 VAL cc_start: 0.8509 (t) cc_final: 0.8304 (p) REVERT: A 423 VAL cc_start: 0.7994 (t) cc_final: 0.7581 (m) outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.1102 time to fit residues: 13.0568 Evaluate side-chains 94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.156946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140787 restraints weight = 5423.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144984 restraints weight = 2947.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147765 restraints weight = 1832.340| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3246 Z= 0.156 Angle : 0.704 8.979 4437 Z= 0.351 Chirality : 0.043 0.329 502 Planarity : 0.004 0.031 529 Dihedral : 13.373 150.158 440 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.20 % Allowed : 24.32 % Favored : 74.47 % 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: 1.32 (0.44), residues: 384 helix: 1.58 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -1.74 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.008 0.002 HIS A 364 PHE 0.017 0.001 PHE A 198 TYR 0.024 0.002 TYR A 445 ARG 0.001 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 220) hydrogen bonds : angle 3.91227 ( 654) covalent geometry : bond 0.00337 ( 3246) covalent geometry : angle 0.70440 ( 4437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1460.19 seconds wall clock time: 25 minutes 55.92 seconds (1555.92 seconds total)