Starting phenix.real_space_refine on Wed Jul 23 08:16:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.map" model { file = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2025/9far_50279.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 23 5.16 5 Cl 1 4.86 5 C 1591 2.51 5 N 341 2.21 5 O 388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2345 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 471 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'P1L:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 255 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "L" Number of atoms: 1515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 193, 1500 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Conformer: "B" Number of residues, atoms: 193, 1500 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} bond proxies already assigned to first conformer: 1523 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'CLR': 1, 'D10': 1, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' CL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.50, per 1000 atoms: 1.49 Number of scatterers: 2345 At special positions: 0 Unit cell: (53.129, 56.3009, 84.0548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 23 16.00 P 1 15.00 O 388 8.00 N 341 7.00 C 1591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 109 " - pdb=" SG CYS L 128 " distance=2.04 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 441.3 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 71.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 401 through 427 removed outlier: 4.243A pdb=" N ILE C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'H' and resid 672 through 699 Processing helix chain 'L' and resid 12 through 43 Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.649A pdb=" N THR L 86 " --> pdb=" O ASP L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 113 Processing helix chain 'L' and resid 114 through 117 removed outlier: 3.623A pdb=" N PHE L 117 " --> pdb=" O SER L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'L' and resid 120 through 146 Processing helix chain 'L' and resid 147 through 151 removed outlier: 4.056A pdb=" N ASP L 151 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 160 Processing helix chain 'L' and resid 174 through 203 removed outlier: 3.786A pdb=" N ILE L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR L 202 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP L 203 " --> pdb=" O ASN L 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 78 157 hydrogen bonds defined for protein. 452 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: 0.66 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 330 1.31 - 1.44: 710 1.44 - 1.56: 1333 1.56 - 1.69: 2 1.69 - 1.82: 32 Bond restraints: 2407 Sorted by residual: bond pdb=" C1 PGW L 301 " pdb=" O01 PGW L 301 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C19 PGW L 301 " pdb=" O03 PGW L 301 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N ASP H 671 " pdb=" CA ASP H 671 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.85e+00 bond pdb=" N VAL H 680 " pdb=" CA VAL H 680 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.54e+00 bond pdb=" N GLU C 383 " pdb=" CA GLU C 383 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.31e-02 5.83e+03 6.50e+00 ... (remaining 2402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 3127 3.04 - 6.09: 102 6.09 - 9.13: 3 9.13 - 12.17: 5 12.17 - 15.22: 2 Bond angle restraints: 3239 Sorted by residual: angle pdb=" CB P1L C 380 " pdb=" SG P1L C 380 " pdb=" C7 P1L C 380 " ideal model delta sigma weight residual 106.10 121.32 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" CA P1L C 380 " pdb=" C P1L C 380 " pdb=" O P1L C 380 " ideal model delta sigma weight residual 128.33 115.14 13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CA ASP C 374 " pdb=" C ASP C 374 " pdb=" O ASP C 374 " ideal model delta sigma weight residual 122.03 117.71 4.32 1.13e+00 7.83e-01 1.46e+01 angle pdb=" CA P1L C 385 " pdb=" C P1L C 385 " pdb=" O P1L C 385 " ideal model delta sigma weight residual 128.33 117.40 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O13 PGW L 301 " pdb=" P PGW L 301 " pdb=" O14 PGW L 301 " ideal model delta sigma weight residual 119.81 109.21 10.60 3.00e+00 1.11e-01 1.25e+01 ... (remaining 3234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 1416 35.60 - 71.20: 32 71.20 - 106.80: 4 106.80 - 142.40: 2 142.40 - 178.00: 1 Dihedral angle restraints: 1455 sinusoidal: 643 harmonic: 812 Sorted by residual: dihedral pdb=" C07 PGW L 301 " pdb=" C06 PGW L 301 " pdb=" C10 PGW L 301 " pdb=" C9 PGW L 301 " ideal model delta sinusoidal sigma weight residual 110.06 -71.94 -178.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O12 PGW L 301 " pdb=" C04 PGW L 301 " pdb=" C05 PGW L 301 " pdb=" OAF PGW L 301 " ideal model delta sinusoidal sigma weight residual 69.27 -157.62 -133.11 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CAD PGW L 301 " pdb=" C04 PGW L 301 " pdb=" C05 PGW L 301 " pdb=" O12 PGW L 301 " ideal model delta sinusoidal sigma weight residual 168.74 37.55 131.19 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 1452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 304 0.071 - 0.142: 44 0.142 - 0.213: 4 0.213 - 0.284: 0 0.284 - 0.355: 3 Chirality restraints: 355 Sorted by residual: chirality pdb=" CA P1L C 385 " pdb=" N P1L C 385 " pdb=" C P1L C 385 " pdb=" CB P1L C 385 " both_signs ideal model delta sigma weight residual False 2.27 2.62 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA P1L C 380 " pdb=" N P1L C 380 " pdb=" C P1L C 380 " pdb=" CB P1L C 380 " both_signs ideal model delta sigma weight residual False 2.27 2.62 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA P1L C 381 " pdb=" N P1L C 381 " pdb=" C P1L C 381 " pdb=" CB P1L C 381 " both_signs ideal model delta sigma weight residual False 2.27 2.59 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 352 not shown) Planarity restraints: 376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA P1L C 380 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C P1L C 380 " -0.063 2.00e-02 2.50e+03 pdb=" O P1L C 380 " 0.023 2.00e-02 2.50e+03 pdb=" N P1L C 381 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 73 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ARG L 73 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG L 73 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU L 74 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 668 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ASP H 668 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP H 668 " 0.009 2.00e-02 2.50e+03 pdb=" N SER H 669 " 0.008 2.00e-02 2.50e+03 ... (remaining 373 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 106 2.73 - 3.27: 2471 3.27 - 3.81: 3762 3.81 - 4.36: 4614 4.36 - 4.90: 7978 Nonbonded interactions: 18931 Sorted by model distance: nonbonded pdb=" O12 PGW L 301 " pdb=" OAE PGW L 301 " model vdw 2.187 3.040 nonbonded pdb=" O PHE L 117 " pdb=" OAE PGW L 301 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR H 672 " pdb=" OD1 ASP L 49 " model vdw 2.400 3.040 nonbonded pdb=" O1 CLR C 502 " pdb="CL CL L 302 " model vdw 2.430 3.190 nonbonded pdb=" O GLY L 79 " pdb=" OG SER L 80 " model vdw 2.458 3.040 ... (remaining 18926 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.310 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.007 0.083 2410 Z= 0.381 Angle : 1.170 15.218 3245 Z= 0.555 Chirality : 0.055 0.355 355 Planarity : 0.004 0.036 376 Dihedral : 17.131 177.997 926 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.87 % Allowed : 2.17 % Favored : 96.96 % 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 (0.53), residues: 266 helix: 1.91 (0.37), residues: 176 sheet: -2.11 (1.41), residues: 13 loop : -1.09 (0.81), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.012 0.001 PHE L 59 TYR 0.013 0.001 TYR L 15 ARG 0.002 0.001 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.12515 ( 157) hydrogen bonds : angle 5.56474 ( 452) SS BOND : bond 0.00360 ( 3) SS BOND : angle 2.25767 ( 6) covalent geometry : bond 0.00679 ( 2407) covalent geometry : angle 1.16724 ( 3239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8785 (t) cc_final: 0.8289 (m) REVERT: H 677 SER cc_start: 0.8810 (t) cc_final: 0.8589 (p) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.5385 time to fit residues: 26.6153 Evaluate side-chains 33 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093337 restraints weight = 15740.770| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 6.43 r_work: 0.2979 rms_B_bonded: 6.38 restraints_weight: 2.0000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2410 Z= 0.162 Angle : 0.641 9.189 3245 Z= 0.319 Chirality : 0.042 0.153 355 Planarity : 0.003 0.024 376 Dihedral : 15.705 154.242 478 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 11.74 % Favored : 86.09 % 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: 1.83 (0.52), residues: 266 helix: 2.44 (0.37), residues: 177 sheet: -1.86 (1.43), residues: 13 loop : -1.27 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.015 0.002 PHE L 117 TYR 0.020 0.002 TYR L 64 ARG 0.002 0.001 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 157) hydrogen bonds : angle 4.20424 ( 452) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.31952 ( 6) covalent geometry : bond 0.00384 ( 2407) covalent geometry : angle 0.63868 ( 3239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8642 (t) cc_final: 0.8348 (m) REVERT: L 55 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8124 (ttpp) REVERT: L 74 GLU cc_start: 0.6877 (mp0) cc_final: 0.6633 (mp0) REVERT: L 151 ASP cc_start: 0.7700 (m-30) cc_final: 0.7477 (m-30) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 0.7701 time to fit residues: 34.3830 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088404 restraints weight = 16562.758| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 5.39 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2410 Z= 0.196 Angle : 0.662 9.479 3245 Z= 0.327 Chirality : 0.043 0.159 355 Planarity : 0.003 0.019 376 Dihedral : 14.541 129.676 476 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.04 % Allowed : 12.61 % Favored : 84.35 % 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: 1.85 (0.52), residues: 266 helix: 2.47 (0.36), residues: 177 sheet: -1.81 (1.45), residues: 13 loop : -1.31 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 PHE 0.011 0.002 PHE L 59 TYR 0.017 0.002 TYR L 15 ARG 0.002 0.001 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 157) hydrogen bonds : angle 4.17629 ( 452) SS BOND : bond 0.00554 ( 3) SS BOND : angle 1.10942 ( 6) covalent geometry : bond 0.00474 ( 2407) covalent geometry : angle 0.66099 ( 3239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8700 (t) cc_final: 0.8338 (m) REVERT: L 74 GLU cc_start: 0.6852 (mp0) cc_final: 0.6488 (mp0) REVERT: L 131 MET cc_start: 0.8245 (mtm) cc_final: 0.8023 (mtp) outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 0.7995 time to fit residues: 38.1238 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.127529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094287 restraints weight = 12842.915| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 6.71 r_work: 0.2923 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2410 Z= 0.179 Angle : 0.638 10.111 3245 Z= 0.316 Chirality : 0.042 0.177 355 Planarity : 0.003 0.019 376 Dihedral : 13.049 92.061 476 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.04 % Allowed : 15.22 % Favored : 81.74 % 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: 1.94 (0.52), residues: 266 helix: 2.60 (0.37), residues: 177 sheet: -2.10 (1.42), residues: 13 loop : -1.38 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 PHE 0.013 0.001 PHE L 117 TYR 0.012 0.001 TYR L 15 ARG 0.002 0.001 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 157) hydrogen bonds : angle 4.14486 ( 452) SS BOND : bond 0.00901 ( 3) SS BOND : angle 2.27415 ( 6) covalent geometry : bond 0.00428 ( 2407) covalent geometry : angle 0.63125 ( 3239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8632 (t) cc_final: 0.8334 (m) REVERT: L 74 GLU cc_start: 0.6782 (mp0) cc_final: 0.6520 (mp0) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.7615 time to fit residues: 30.1757 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain H residue 685 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096385 restraints weight = 12081.642| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 6.47 r_work: 0.2954 rms_B_bonded: 6.05 restraints_weight: 2.0000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2410 Z= 0.136 Angle : 0.604 10.490 3245 Z= 0.296 Chirality : 0.039 0.139 355 Planarity : 0.003 0.019 376 Dihedral : 11.885 59.731 476 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.61 % Allowed : 16.09 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.52), residues: 266 helix: 2.87 (0.36), residues: 176 sheet: -1.85 (1.38), residues: 13 loop : -1.54 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.011 0.001 PHE L 59 TYR 0.011 0.001 TYR C 421 ARG 0.002 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 157) hydrogen bonds : angle 3.93194 ( 452) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.63427 ( 6) covalent geometry : bond 0.00317 ( 2407) covalent geometry : angle 0.60033 ( 3239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8656 (t) cc_final: 0.8357 (m) REVERT: L 74 GLU cc_start: 0.6633 (mp0) cc_final: 0.6403 (mp0) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.6340 time to fit residues: 25.2521 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain H residue 685 SER Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089919 restraints weight = 14933.987| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.92 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2410 Z= 0.143 Angle : 0.625 11.184 3245 Z= 0.304 Chirality : 0.040 0.140 355 Planarity : 0.003 0.018 376 Dihedral : 11.799 60.884 476 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 16.96 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.52), residues: 266 helix: 2.88 (0.36), residues: 176 sheet: -1.92 (1.38), residues: 13 loop : -1.54 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.015 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.002 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 157) hydrogen bonds : angle 3.93502 ( 452) SS BOND : bond 0.00536 ( 3) SS BOND : angle 1.25550 ( 6) covalent geometry : bond 0.00337 ( 2407) covalent geometry : angle 0.62316 ( 3239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8694 (t) cc_final: 0.8309 (m) REVERT: L 74 GLU cc_start: 0.6730 (mp0) cc_final: 0.6464 (mp0) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.6537 time to fit residues: 27.4918 Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain H residue 685 SER Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.128112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095758 restraints weight = 18055.291| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 7.33 r_work: 0.2923 rms_B_bonded: 6.50 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2410 Z= 0.140 Angle : 0.626 11.801 3245 Z= 0.302 Chirality : 0.040 0.139 355 Planarity : 0.003 0.019 376 Dihedral : 11.503 62.199 476 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.04 % Allowed : 17.39 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.52), residues: 266 helix: 2.97 (0.36), residues: 172 sheet: -1.91 (1.38), residues: 13 loop : -1.59 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.015 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.001 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 157) hydrogen bonds : angle 3.91388 ( 452) SS BOND : bond 0.00418 ( 3) SS BOND : angle 1.02506 ( 6) covalent geometry : bond 0.00332 ( 2407) covalent geometry : angle 0.62478 ( 3239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.245 Fit side-chains REVERT: H 673 SER cc_start: 0.8661 (t) cc_final: 0.8354 (m) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.6349 time to fit residues: 24.6106 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain H residue 685 SER Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.127982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086855 restraints weight = 20930.327| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.98 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2410 Z= 0.142 Angle : 0.655 12.517 3245 Z= 0.314 Chirality : 0.040 0.139 355 Planarity : 0.003 0.019 376 Dihedral : 11.320 63.845 476 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.48 % Allowed : 18.26 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.52), residues: 266 helix: 3.00 (0.36), residues: 172 sheet: -1.94 (1.39), residues: 13 loop : -1.51 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.016 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.001 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 157) hydrogen bonds : angle 3.91848 ( 452) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.90043 ( 6) covalent geometry : bond 0.00333 ( 2407) covalent geometry : angle 0.65407 ( 3239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.357 Fit side-chains REVERT: H 673 SER cc_start: 0.8689 (t) cc_final: 0.8311 (m) REVERT: L 16 MET cc_start: 0.6204 (tmm) cc_final: 0.5920 (tpt) outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 0.6454 time to fit residues: 25.6643 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088743 restraints weight = 16547.823| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 5.18 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2410 Z= 0.151 Angle : 0.668 11.767 3245 Z= 0.319 Chirality : 0.040 0.142 355 Planarity : 0.003 0.019 376 Dihedral : 11.334 66.372 476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.61 % Allowed : 18.26 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.52), residues: 266 helix: 2.85 (0.36), residues: 176 sheet: -2.02 (1.33), residues: 13 loop : -1.44 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.015 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.002 0.000 ARG L 73 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 157) hydrogen bonds : angle 3.96854 ( 452) SS BOND : bond 0.00478 ( 3) SS BOND : angle 0.89080 ( 6) covalent geometry : bond 0.00361 ( 2407) covalent geometry : angle 0.66751 ( 3239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.235 Fit side-chains REVERT: H 673 SER cc_start: 0.8637 (t) cc_final: 0.8241 (m) REVERT: L 74 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6662 (mp0) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.7245 time to fit residues: 27.8875 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 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 = 0.3774 r_free = 0.3774 target = 0.127867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087992 restraints weight = 10962.012| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.85 r_work: 0.3004 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2410 Z= 0.147 Angle : 0.683 13.293 3245 Z= 0.322 Chirality : 0.041 0.139 355 Planarity : 0.003 0.020 376 Dihedral : 11.252 67.355 476 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.30 % Allowed : 20.00 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.52), residues: 266 helix: 2.81 (0.36), residues: 176 sheet: -2.08 (1.30), residues: 13 loop : -1.39 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 PHE 0.015 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.001 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 157) hydrogen bonds : angle 4.03535 ( 452) SS BOND : bond 0.00468 ( 3) SS BOND : angle 0.82433 ( 6) covalent geometry : bond 0.00352 ( 2407) covalent geometry : angle 0.68226 ( 3239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.263 Fit side-chains REVERT: H 673 SER cc_start: 0.8679 (t) cc_final: 0.8346 (m) REVERT: L 16 MET cc_start: 0.6381 (tmm) cc_final: 0.6085 (tpt) REVERT: L 74 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6559 (mp0) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.6777 time to fit residues: 24.8270 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.128665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096117 restraints weight = 16935.853| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 6.84 r_work: 0.2934 rms_B_bonded: 6.34 restraints_weight: 2.0000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2410 Z= 0.139 Angle : 0.675 12.896 3245 Z= 0.319 Chirality : 0.040 0.139 355 Planarity : 0.003 0.019 376 Dihedral : 11.069 68.467 476 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 19.57 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.53), residues: 266 helix: 2.86 (0.36), residues: 176 sheet: -2.00 (1.34), residues: 13 loop : -1.34 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 150 HIS 0.002 0.001 HIS L 14 PHE 0.014 0.001 PHE L 117 TYR 0.011 0.001 TYR C 421 ARG 0.001 0.000 ARG H 670 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 157) hydrogen bonds : angle 4.01102 ( 452) SS BOND : bond 0.00441 ( 3) SS BOND : angle 0.78436 ( 6) covalent geometry : bond 0.00329 ( 2407) covalent geometry : angle 0.67465 ( 3239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.96 seconds wall clock time: 38 minutes 27.26 seconds (2307.26 seconds total)