Starting phenix.real_space_refine on Wed Sep 17 03:00:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9far_50279/09_2025/9far_50279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9far_50279/09_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_50279/09_2025/9far_50279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9far_50279/09_2025/9far_50279.map" model { file = "/net/cci-nas-00/data/ceres_data/9far_50279/09_2025/9far_50279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9far_50279/09_2025/9far_50279.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.29, per 1000 atoms: 0.55 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: 0.45 Conformation dependent library (CDL) restraints added in 135.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.10 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: 0.42 Time building geometry restraints manager: 0.38 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.860 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.001 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.012 0.001 PHE L 59 TRP 0.006 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 2407) covalent geometry : angle 1.16724 ( 3239) SS BOND : bond 0.00360 ( 3) SS BOND : angle 2.25767 ( 6) hydrogen bonds : bond 0.12515 ( 157) hydrogen bonds : angle 5.56474 ( 452) *********************** 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 : 0.089 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: 0.2777 time to fit residues: 13.6563 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 : 0.099 ------------------------------------------------------------------------------- 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 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.132131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093698 restraints weight = 17501.779| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 6.57 r_work: 0.2978 rms_B_bonded: 6.52 restraints_weight: 2.0000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2410 Z= 0.160 Angle : 0.636 9.058 3245 Z= 0.318 Chirality : 0.043 0.180 355 Planarity : 0.004 0.024 376 Dihedral : 15.732 154.582 478 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 10.87 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.52), residues: 266 helix: 2.43 (0.37), residues: 177 sheet: -1.85 (1.44), residues: 13 loop : -1.26 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.020 0.002 TYR L 64 PHE 0.016 0.002 PHE L 117 TRP 0.009 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2407) covalent geometry : angle 0.63372 ( 3239) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.35871 ( 6) hydrogen bonds : bond 0.04201 ( 157) hydrogen bonds : angle 4.18999 ( 452) *********************** 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: 6 poor density : 38 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: C 404 SER cc_start: 0.9017 (t) cc_final: 0.8744 (p) REVERT: H 673 SER cc_start: 0.8616 (t) cc_final: 0.8333 (m) REVERT: H 699 TYR cc_start: 0.6034 (t80) cc_final: 0.5832 (t80) REVERT: L 55 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8102 (ttpp) REVERT: L 74 GLU cc_start: 0.6889 (mp0) cc_final: 0.6626 (mp0) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.3722 time to fit residues: 16.5689 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.131069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097610 restraints weight = 16249.690| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 7.41 r_work: 0.2966 rms_B_bonded: 6.61 restraints_weight: 2.0000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2410 Z= 0.137 Angle : 0.598 9.467 3245 Z= 0.296 Chirality : 0.040 0.146 355 Planarity : 0.003 0.020 376 Dihedral : 14.132 132.957 476 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.52), residues: 266 helix: 2.69 (0.37), residues: 177 sheet: -1.71 (1.44), residues: 13 loop : -1.26 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 407 TYR 0.016 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2407) covalent geometry : angle 0.59710 ( 3239) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.90445 ( 6) hydrogen bonds : bond 0.03912 ( 157) hydrogen bonds : angle 3.99938 ( 452) *********************** 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 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8626 (t) cc_final: 0.8367 (m) REVERT: L 74 GLU cc_start: 0.6796 (mp0) cc_final: 0.6571 (mp0) REVERT: L 148 ASP cc_start: 0.8672 (t0) cc_final: 0.8443 (t0) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.4215 time to fit residues: 17.8713 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 0.0000 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 690 ASN L 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097121 restraints weight = 14778.053| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 7.11 r_work: 0.2962 rms_B_bonded: 6.44 restraints_weight: 2.0000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2410 Z= 0.133 Angle : 0.597 10.131 3245 Z= 0.295 Chirality : 0.040 0.164 355 Planarity : 0.003 0.020 376 Dihedral : 12.973 98.476 476 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 14.78 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.52), residues: 266 helix: 2.77 (0.37), residues: 177 sheet: -2.05 (1.38), residues: 13 loop : -1.29 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.016 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.010 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2407) covalent geometry : angle 0.58902 ( 3239) SS BOND : bond 0.00718 ( 3) SS BOND : angle 2.27720 ( 6) hydrogen bonds : bond 0.03955 ( 157) hydrogen bonds : angle 4.00742 ( 452) *********************** 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 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8616 (t) cc_final: 0.8336 (m) REVERT: L 16 MET cc_start: 0.6243 (tmm) cc_final: 0.5962 (tmt) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.2953 time to fit residues: 12.6616 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.128689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096806 restraints weight = 13068.939| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 6.70 r_work: 0.2948 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2410 Z= 0.142 Angle : 0.610 8.448 3245 Z= 0.301 Chirality : 0.040 0.140 355 Planarity : 0.003 0.019 376 Dihedral : 11.779 58.668 476 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.52), residues: 266 helix: 2.83 (0.37), residues: 177 sheet: -1.80 (1.39), residues: 13 loop : -1.36 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 73 TYR 0.014 0.001 TYR L 15 PHE 0.010 0.001 PHE L 59 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2407) covalent geometry : angle 0.60606 ( 3239) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.65060 ( 6) hydrogen bonds : bond 0.03921 ( 157) hydrogen bonds : angle 3.94921 ( 452) *********************** 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 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: C 407 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.4379 (mmt90) REVERT: H 673 SER cc_start: 0.8635 (t) cc_final: 0.8333 (m) REVERT: L 16 MET cc_start: 0.6335 (tmm) cc_final: 0.6095 (tmt) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.3547 time to fit residues: 15.0988 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain H residue 686 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.130077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092421 restraints weight = 17320.642| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.38 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3014 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= 0.121 Angle : 0.596 7.614 3245 Z= 0.295 Chirality : 0.039 0.139 355 Planarity : 0.003 0.019 376 Dihedral : 11.175 58.701 476 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 16.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.52), residues: 266 helix: 2.91 (0.37), residues: 177 sheet: -1.74 (1.39), residues: 13 loop : -1.45 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.011 0.001 PHE L 117 TRP 0.005 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2407) covalent geometry : angle 0.59409 ( 3239) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.13544 ( 6) hydrogen bonds : bond 0.03792 ( 157) hydrogen bonds : angle 3.85787 ( 452) *********************** 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 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.092 Fit side-chains REVERT: H 673 SER cc_start: 0.8650 (t) cc_final: 0.8274 (m) REVERT: L 16 MET cc_start: 0.6432 (tmm) cc_final: 0.6225 (tmt) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.3492 time to fit residues: 14.1779 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.129021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089517 restraints weight = 20807.835| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 5.82 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2410 Z= 0.146 Angle : 0.620 7.214 3245 Z= 0.305 Chirality : 0.040 0.141 355 Planarity : 0.003 0.019 376 Dihedral : 11.338 59.241 476 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.48 % Allowed : 17.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.52), residues: 266 helix: 2.85 (0.37), residues: 177 sheet: -1.60 (1.42), residues: 13 loop : -1.49 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.009 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2407) covalent geometry : angle 0.61901 ( 3239) SS BOND : bond 0.00513 ( 3) SS BOND : angle 1.05523 ( 6) hydrogen bonds : bond 0.03894 ( 157) hydrogen bonds : angle 3.97614 ( 452) *********************** 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 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.088 Fit side-chains REVERT: C 407 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.4313 (mmt90) REVERT: H 673 SER cc_start: 0.8707 (t) cc_final: 0.8339 (m) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.3722 time to fit residues: 15.7838 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 416 LEU 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 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.128187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095763 restraints weight = 16355.387| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 6.89 r_work: 0.2926 rms_B_bonded: 6.39 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2410 Z= 0.139 Angle : 0.625 8.159 3245 Z= 0.307 Chirality : 0.040 0.139 355 Planarity : 0.003 0.021 376 Dihedral : 11.307 59.559 476 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.61 % Allowed : 20.00 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.52), residues: 266 helix: 2.97 (0.37), residues: 172 sheet: -1.70 (1.39), residues: 13 loop : -1.57 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2407) covalent geometry : angle 0.62404 ( 3239) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.94356 ( 6) hydrogen bonds : bond 0.03840 ( 157) hydrogen bonds : angle 3.94776 ( 452) *********************** 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: 6 poor density : 33 time to evaluate : 0.080 Fit side-chains REVERT: C 407 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.4372 (mmt90) REVERT: H 673 SER cc_start: 0.8637 (t) cc_final: 0.8328 (m) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.3611 time to fit residues: 14.1705 Evaluate side-chains 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 416 LEU 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 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.126678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094310 restraints weight = 15581.088| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 6.73 r_work: 0.2901 rms_B_bonded: 6.34 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2410 Z= 0.159 Angle : 0.656 8.013 3245 Z= 0.323 Chirality : 0.041 0.140 355 Planarity : 0.003 0.016 376 Dihedral : 11.377 61.186 476 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.91 % Allowed : 18.26 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.52), residues: 266 helix: 2.83 (0.37), residues: 172 sheet: -1.71 (1.39), residues: 13 loop : -1.59 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.013 0.001 PHE L 117 TRP 0.010 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2407) covalent geometry : angle 0.65531 ( 3239) SS BOND : bond 0.00508 ( 3) SS BOND : angle 0.99314 ( 6) hydrogen bonds : bond 0.03960 ( 157) hydrogen bonds : angle 4.03494 ( 452) *********************** 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 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.054 Fit side-chains REVERT: C 407 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.4337 (mmt90) REVERT: H 673 SER cc_start: 0.8667 (t) cc_final: 0.8339 (m) outliers start: 9 outliers final: 3 residues processed: 40 average time/residue: 0.3232 time to fit residues: 13.3605 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE 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 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094924 restraints weight = 15725.484| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 6.79 r_work: 0.2915 rms_B_bonded: 6.28 restraints_weight: 2.0000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 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 = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3413 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= 0.151 Angle : 0.663 8.003 3245 Z= 0.324 Chirality : 0.041 0.158 355 Planarity : 0.003 0.016 376 Dihedral : 11.227 61.791 476 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.17 % Allowed : 20.87 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.52), residues: 266 helix: 2.81 (0.36), residues: 172 sheet: -1.62 (1.42), residues: 13 loop : -1.55 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2407) covalent geometry : angle 0.66263 ( 3239) SS BOND : bond 0.00464 ( 3) SS BOND : angle 0.90583 ( 6) hydrogen bonds : bond 0.03924 ( 157) hydrogen bonds : angle 4.05480 ( 452) ********************** 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 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.089 Fit side-chains REVERT: C 407 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.4323 (mmt90) REVERT: H 673 SER cc_start: 0.8666 (t) cc_final: 0.8343 (m) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.3651 time to fit residues: 13.5916 Evaluate side-chains 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 416 LEU 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 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.0870 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091660 restraints weight = 11250.635| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.46 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2410 Z= 0.129 Angle : 0.642 9.077 3245 Z= 0.312 Chirality : 0.040 0.150 355 Planarity : 0.003 0.017 376 Dihedral : 10.820 61.823 476 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.74 % Allowed : 21.30 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.52), residues: 266 helix: 2.92 (0.37), residues: 172 sheet: -1.66 (1.41), residues: 13 loop : -1.49 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.005 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2407) covalent geometry : angle 0.64121 ( 3239) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.81177 ( 6) hydrogen bonds : bond 0.03814 ( 157) hydrogen bonds : angle 3.98473 ( 452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.75 seconds wall clock time: 20 minutes 7.80 seconds (1207.80 seconds total)