Starting phenix.real_space_refine on Fri Aug 22 12:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pij_17683/08_2025/8pij_17683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pij_17683/08_2025/8pij_17683.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/8pij_17683/08_2025/8pij_17683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pij_17683/08_2025/8pij_17683.map" model { file = "/net/cci-nas-00/data/ceres_data/8pij_17683/08_2025/8pij_17683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pij_17683/08_2025/8pij_17683.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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.02, per 1000 atoms: 0.47 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 94.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 24.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.404A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.906A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.582A pdb=" N VAL B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 222 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: 0.41 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA MET B 116 " pdb=" C MET B 116 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" CA VAL B 110 " pdb=" C VAL B 110 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" CA SER B 115 " pdb=" C SER B 115 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.34e-02 5.57e+03 5.89e+00 bond pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 1.521 1.497 0.025 1.23e-02 6.61e+03 3.99e+00 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2968 1.85 - 3.70: 40 3.70 - 5.55: 8 5.55 - 7.40: 2 7.40 - 9.25: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 1217 24.62 - 49.23: 108 49.23 - 73.84: 26 73.84 - 98.46: 0 98.46 - 123.07: 2 Dihedral angle restraints: 1353 sinusoidal: 524 harmonic: 829 Sorted by residual: dihedral pdb=" C8 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual 173.56 -63.37 -123.07 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O4 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual -63.24 56.71 -119.95 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 185 0.023 - 0.046: 77 0.046 - 0.069: 52 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1773 3.30 - 3.83: 3372 3.83 - 4.37: 3797 4.37 - 4.90: 6913 Nonbonded interactions: 16220 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 3.040 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 3.040 ... (remaining 16215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.004 0.118 2231 Z= 0.281 Angle : 0.579 9.250 3025 Z= 0.291 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 18.971 123.074 814 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % 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: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.018 0.001 TYR B 113 PHE 0.002 0.001 PHE A 119 TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 2226) covalent geometry : angle 0.57804 ( 3019) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.04455 ( 6) hydrogen bonds : bond 0.22915 ( 85) hydrogen bonds : angle 7.08206 ( 222) Misc. bond : bond 0.04089 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.4632 time to fit residues: 29.4154 Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3051 r_free = 0.3051 target = 0.060440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.040073 restraints weight = 6488.111| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.19 r_work: 0.2390 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2280 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2231 Z= 0.215 Angle : 0.556 4.459 3025 Z= 0.296 Chirality : 0.044 0.145 349 Planarity : 0.003 0.025 383 Dihedral : 8.449 81.030 350 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.06 % Allowed : 32.90 % Favored : 61.04 % 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: 0.21 (0.52), residues: 284 helix: 1.03 (0.74), residues: 51 sheet: 0.35 (0.55), residues: 92 loop : -0.25 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.008 0.001 TYR B 118 PHE 0.009 0.001 PHE B 102 TRP 0.013 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 2226) covalent geometry : angle 0.55663 ( 3019) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.37386 ( 6) hydrogen bonds : bond 0.05117 ( 85) hydrogen bonds : angle 4.80617 ( 222) Misc. bond : bond 0.00083 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.103 Fit side-chains REVERT: A 41 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: A 126 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8704 (ttt180) REVERT: B 20 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7232 (mp) REVERT: B 75 ASP cc_start: 0.8365 (t0) cc_final: 0.7414 (t70) REVERT: B 84 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8191 (tp40) REVERT: B 85 MET cc_start: 0.8344 (mtt) cc_final: 0.8037 (mtt) REVERT: B 93 THR cc_start: 0.9344 (p) cc_final: 0.9093 (m) outliers start: 14 outliers final: 4 residues processed: 48 average time/residue: 0.5365 time to fit residues: 26.3418 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.041592 restraints weight = 6416.228| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.16 r_work: 0.2441 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2231 Z= 0.103 Angle : 0.492 7.074 3025 Z= 0.256 Chirality : 0.041 0.147 349 Planarity : 0.003 0.025 383 Dihedral : 5.236 52.360 346 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.63 % Allowed : 31.17 % Favored : 63.20 % 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: 0.27 (0.52), residues: 284 helix: 1.26 (0.76), residues: 51 sheet: 0.26 (0.52), residues: 92 loop : -0.19 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.008 0.001 TYR B 118 PHE 0.005 0.001 PHE B 102 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 2226) covalent geometry : angle 0.49189 ( 3019) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.41849 ( 6) hydrogen bonds : bond 0.03474 ( 85) hydrogen bonds : angle 4.27060 ( 222) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.081 Fit side-chains REVERT: A 41 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: B 75 ASP cc_start: 0.8440 (t0) cc_final: 0.7859 (t0) REVERT: B 84 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8285 (tp40) REVERT: B 85 MET cc_start: 0.8395 (mtt) cc_final: 0.8183 (mtt) outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.5386 time to fit residues: 26.9591 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.058677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.038017 restraints weight = 6461.131| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 3.16 r_work: 0.2336 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 2231 Z= 0.313 Angle : 0.619 6.118 3025 Z= 0.325 Chirality : 0.046 0.140 349 Planarity : 0.003 0.026 383 Dihedral : 5.783 50.878 346 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.93 % Allowed : 27.71 % Favored : 65.37 % 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: -0.03 (0.49), residues: 284 helix: 0.97 (0.73), residues: 51 sheet: 0.38 (0.54), residues: 77 loop : -0.52 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.009 0.001 TYR B 82 PHE 0.006 0.002 PHE B 102 TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00743 ( 2226) covalent geometry : angle 0.61884 ( 3019) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.43656 ( 6) hydrogen bonds : bond 0.05623 ( 85) hydrogen bonds : angle 4.51341 ( 222) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.092 Fit side-chains REVERT: A 41 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: B 40 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8934 (ttp-170) REVERT: B 75 ASP cc_start: 0.8436 (t0) cc_final: 0.7920 (t0) REVERT: B 85 MET cc_start: 0.8491 (mtt) cc_final: 0.8258 (mtt) REVERT: B 103 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7383 (mmp80) outliers start: 16 outliers final: 6 residues processed: 50 average time/residue: 0.5903 time to fit residues: 30.1023 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.059878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.039258 restraints weight = 6516.388| |-----------------------------------------------------------------------------| r_work (start): 0.2487 rms_B_bonded: 3.18 r_work: 0.2373 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2231 Z= 0.173 Angle : 0.549 6.789 3025 Z= 0.285 Chirality : 0.043 0.141 349 Planarity : 0.003 0.026 383 Dihedral : 5.406 51.013 346 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 29.87 % Favored : 65.37 % 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: 0.21 (0.50), residues: 284 helix: 1.34 (0.75), residues: 51 sheet: 0.53 (0.55), residues: 77 loop : -0.44 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.007 0.001 TYR B 118 PHE 0.006 0.001 PHE B 102 TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2226) covalent geometry : angle 0.54918 ( 3019) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.36744 ( 6) hydrogen bonds : bond 0.04280 ( 85) hydrogen bonds : angle 4.22047 ( 222) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.105 Fit side-chains REVERT: A 41 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: B 40 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8843 (ttp-170) REVERT: B 75 ASP cc_start: 0.8422 (t0) cc_final: 0.7849 (t70) REVERT: B 84 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8353 (tp40) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.5920 time to fit residues: 27.7875 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.060213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.039770 restraints weight = 6374.393| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 3.16 r_work: 0.2389 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2280 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2231 Z= 0.139 Angle : 0.531 6.150 3025 Z= 0.281 Chirality : 0.043 0.141 349 Planarity : 0.003 0.029 383 Dihedral : 5.234 50.878 346 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 30.30 % Favored : 65.37 % 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: 0.39 (0.50), residues: 284 helix: 1.55 (0.76), residues: 51 sheet: 0.76 (0.56), residues: 76 loop : -0.40 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.007 0.001 TYR B 118 PHE 0.005 0.001 PHE B 102 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2226) covalent geometry : angle 0.53163 ( 3019) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.37727 ( 6) hydrogen bonds : bond 0.03801 ( 85) hydrogen bonds : angle 4.12913 ( 222) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.080 Fit side-chains REVERT: A 41 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8636 (tm-30) REVERT: B 40 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8803 (ttp-170) REVERT: B 41 GLN cc_start: 0.8460 (tp-100) cc_final: 0.7763 (tp40) REVERT: B 75 ASP cc_start: 0.8416 (t0) cc_final: 0.7851 (t70) REVERT: B 84 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8393 (tp40) REVERT: B 85 MET cc_start: 0.8285 (mtt) cc_final: 0.8064 (mtt) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.5284 time to fit residues: 24.2567 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.060517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.039993 restraints weight = 6423.416| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 3.18 r_work: 0.2397 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2231 Z= 0.128 Angle : 0.551 7.583 3025 Z= 0.282 Chirality : 0.042 0.141 349 Planarity : 0.003 0.030 383 Dihedral : 5.152 50.874 346 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 31.60 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.51), residues: 284 helix: 1.67 (0.76), residues: 51 sheet: 0.73 (0.57), residues: 77 loop : -0.34 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.007 0.001 TYR B 96 PHE 0.005 0.001 PHE B 102 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2226) covalent geometry : angle 0.55116 ( 3019) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.39067 ( 6) hydrogen bonds : bond 0.03648 ( 85) hydrogen bonds : angle 4.07290 ( 222) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.052 Fit side-chains REVERT: A 41 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: B 40 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (ttp-170) REVERT: B 41 GLN cc_start: 0.8467 (tp-100) cc_final: 0.7759 (tp40) REVERT: B 75 ASP cc_start: 0.8397 (t0) cc_final: 0.7821 (t70) REVERT: B 84 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8376 (mm-40) REVERT: B 85 MET cc_start: 0.8319 (mtt) cc_final: 0.7857 (mtt) REVERT: B 103 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7400 (mmp80) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.4071 time to fit residues: 18.2585 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.060728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.040211 restraints weight = 6420.552| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.17 r_work: 0.2403 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2293 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2231 Z= 0.119 Angle : 0.524 5.968 3025 Z= 0.274 Chirality : 0.042 0.136 349 Planarity : 0.003 0.032 383 Dihedral : 5.056 50.755 346 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 30.74 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.51), residues: 284 helix: 1.78 (0.77), residues: 51 sheet: 0.76 (0.55), residues: 82 loop : -0.36 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.006 0.001 TYR B 118 PHE 0.005 0.001 PHE A 119 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2226) covalent geometry : angle 0.52432 ( 3019) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.38240 ( 6) hydrogen bonds : bond 0.03429 ( 85) hydrogen bonds : angle 3.99892 ( 222) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.114 Fit side-chains REVERT: A 41 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: B 40 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8916 (ttp-170) REVERT: B 41 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7810 (tp40) REVERT: B 75 ASP cc_start: 0.8444 (t0) cc_final: 0.7849 (t70) REVERT: B 84 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8421 (mm-40) REVERT: B 85 MET cc_start: 0.8373 (mtt) cc_final: 0.7884 (mtt) REVERT: B 103 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7425 (mmp80) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.5114 time to fit residues: 23.4754 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.059624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.038945 restraints weight = 6541.173| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 3.20 r_work: 0.2367 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2231 Z= 0.184 Angle : 0.590 7.690 3025 Z= 0.301 Chirality : 0.044 0.134 349 Planarity : 0.003 0.033 383 Dihedral : 5.288 50.639 346 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 29.87 % Favored : 65.37 % 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: 0.37 (0.50), residues: 284 helix: 1.60 (0.76), residues: 51 sheet: 0.70 (0.57), residues: 77 loop : -0.42 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.007 0.001 TYR B 82 PHE 0.006 0.001 PHE B 102 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 2226) covalent geometry : angle 0.59047 ( 3019) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.37454 ( 6) hydrogen bonds : bond 0.04363 ( 85) hydrogen bonds : angle 4.15648 ( 222) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.102 Fit side-chains REVERT: A 41 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8608 (tm-30) REVERT: B 40 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8868 (ttp-170) REVERT: B 41 GLN cc_start: 0.8460 (tp-100) cc_final: 0.7781 (tp40) REVERT: B 75 ASP cc_start: 0.8443 (t0) cc_final: 0.7820 (t70) REVERT: B 84 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8406 (mm-40) REVERT: B 85 MET cc_start: 0.8334 (mtt) cc_final: 0.7791 (mtt) REVERT: B 103 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7395 (mmp80) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.5182 time to fit residues: 24.3211 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.059716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.039058 restraints weight = 6527.710| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 3.19 r_work: 0.2372 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2231 Z= 0.174 Angle : 0.577 6.318 3025 Z= 0.300 Chirality : 0.043 0.141 349 Planarity : 0.003 0.032 383 Dihedral : 5.314 50.711 346 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 30.74 % Favored : 64.94 % 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: 0.40 (0.50), residues: 284 helix: 1.61 (0.75), residues: 51 sheet: 0.75 (0.58), residues: 77 loop : -0.42 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.007 0.001 TYR B 118 PHE 0.005 0.001 PHE A 119 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 2226) covalent geometry : angle 0.57692 ( 3019) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.38278 ( 6) hydrogen bonds : bond 0.04178 ( 85) hydrogen bonds : angle 4.14134 ( 222) Misc. bond : bond 0.00070 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.053 Fit side-chains REVERT: A 41 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: B 40 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8839 (ttp-170) REVERT: B 41 GLN cc_start: 0.8465 (tp-100) cc_final: 0.7774 (tp40) REVERT: B 75 ASP cc_start: 0.8492 (t0) cc_final: 0.7858 (t70) REVERT: B 84 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8385 (mm-40) REVERT: B 85 MET cc_start: 0.8356 (mtt) cc_final: 0.7801 (mtt) REVERT: B 103 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7386 (mmp80) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.5554 time to fit residues: 25.4155 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.0570 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.062429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.041949 restraints weight = 6637.430| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 3.24 r_work: 0.2460 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2351 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2231 Z= 0.096 Angle : 0.558 8.263 3025 Z= 0.281 Chirality : 0.041 0.141 349 Planarity : 0.003 0.035 383 Dihedral : 4.933 50.740 346 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.46 % Allowed : 31.60 % Favored : 64.94 % 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: 0.71 (0.51), residues: 284 helix: 1.90 (0.78), residues: 51 sheet: 0.88 (0.54), residues: 81 loop : -0.21 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.006 0.001 TYR B 96 PHE 0.004 0.001 PHE A 119 TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 2226) covalent geometry : angle 0.55841 ( 3019) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.46744 ( 6) hydrogen bonds : bond 0.02558 ( 85) hydrogen bonds : angle 3.83656 ( 222) Misc. bond : bond 0.00021 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.87 seconds wall clock time: 21 minutes 45.61 seconds (1305.61 seconds total)