Starting phenix.real_space_refine on Wed Sep 17 05:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivk_60929/09_2025/9ivk_60929_neut.cif" } resolution = 2.74 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1806 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2640 2.51 5 N 654 2.21 5 O 769 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: 4077 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2271 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 3, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} bond proxies already assigned to first conformer: 953 Chain: "L" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 833 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KY6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.35, per 1000 atoms: 0.33 Number of scatterers: 4077 At special positions: 0 Unit cell: (54.72, 72.96, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 769 8.00 N 654 7.00 C 2640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG ACYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG BCYS H 99 " distance=2.03 Simple disulfide: pdb=" SG ACYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG BCYS L 24 " 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: 0.31 Conformation dependent library (CDL) restraints added in 170.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 56.4% alpha, 24.9% 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 1 through 36 removed outlier: 4.467A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 48 through 110 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.567A pdb=" N VAL A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 removed outlier: 3.572A pdb=" N GLU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 192 through 243 Processing helix chain 'A' and resid 248 through 285 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.866A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.100A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.571A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER H 55 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR H 116 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.571A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER H 55 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.858A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.858A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 923 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: 0.68 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 681 1.28 - 1.41: 1010 1.41 - 1.55: 2446 1.55 - 1.68: 3 1.68 - 1.81: 22 Bond restraints: 4162 Sorted by residual: bond pdb=" C ILE A 50 " pdb=" O ILE A 50 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" N ILE A 48 " pdb=" CA ILE A 48 " ideal model delta sigma weight residual 1.456 1.491 -0.034 9.50e-03 1.11e+04 1.31e+01 bond pdb=" N ILE A 241 " pdb=" CA ILE A 241 " ideal model delta sigma weight residual 1.452 1.494 -0.041 1.18e-02 7.18e+03 1.24e+01 bond pdb=" N ILE A 8 " pdb=" CA ILE A 8 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N LYS A 239 " pdb=" CA LYS A 239 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.33e-02 5.65e+03 9.97e+00 ... (remaining 4157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 5441 2.39 - 4.78: 173 4.78 - 7.17: 13 7.17 - 9.56: 0 9.56 - 11.95: 3 Bond angle restraints: 5630 Sorted by residual: angle pdb=" N LYS A 49 " pdb=" CA LYS A 49 " pdb=" C LYS A 49 " ideal model delta sigma weight residual 113.19 101.24 11.95 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N ILE A 48 " pdb=" CA ILE A 48 " pdb=" C ILE A 48 " ideal model delta sigma weight residual 113.53 103.86 9.67 9.80e-01 1.04e+00 9.74e+01 angle pdb=" N LYS A 240 " pdb=" CA LYS A 240 " pdb=" C LYS A 240 " ideal model delta sigma weight residual 113.01 102.76 10.25 1.20e+00 6.94e-01 7.29e+01 angle pdb=" N PHE A 10 " pdb=" CA PHE A 10 " pdb=" C PHE A 10 " ideal model delta sigma weight residual 111.36 105.57 5.79 1.09e+00 8.42e-01 2.82e+01 angle pdb=" CA THR A 238 " pdb=" C THR A 238 " pdb=" O THR A 238 " ideal model delta sigma weight residual 120.82 115.70 5.12 1.05e+00 9.07e-01 2.38e+01 ... (remaining 5625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 2249 17.53 - 35.06: 209 35.06 - 52.59: 34 52.59 - 70.13: 9 70.13 - 87.66: 12 Dihedral angle restraints: 2513 sinusoidal: 1011 harmonic: 1502 Sorted by residual: dihedral pdb=" CB ACYS L 24 " pdb=" SG ACYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 56.56 36.44 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" C LYS A 239 " pdb=" N LYS A 239 " pdb=" CA LYS A 239 " pdb=" CB LYS A 239 " ideal model delta harmonic sigma weight residual -122.60 -131.80 9.20 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG ACYS H 99 " pdb=" CB ACYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 63.37 29.63 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 2510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 510 0.060 - 0.120: 84 0.120 - 0.180: 26 0.180 - 0.240: 8 0.240 - 0.299: 5 Chirality restraints: 633 Sorted by residual: chirality pdb=" CA LYS A 239 " pdb=" N LYS A 239 " pdb=" C LYS A 239 " pdb=" CB LYS A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS A 49 " pdb=" N LYS A 49 " pdb=" C LYS A 49 " pdb=" CB LYS A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 630 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 242 " -0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LYS A 242 " 0.076 2.00e-02 2.50e+03 pdb=" O LYS A 242 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU A 243 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 236 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C PHE A 236 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A 236 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 237 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 9 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C LEU A 9 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 9 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 10 " 0.017 2.00e-02 2.50e+03 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 649 2.76 - 3.30: 3955 3.30 - 3.83: 6991 3.83 - 4.37: 8130 4.37 - 4.90: 13792 Nonbonded interactions: 33517 Sorted by model distance: nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS A 41 " pdb=" OD1 ASN A 245 " model vdw 2.253 3.120 nonbonded pdb=" NE2 GLN L 91 " pdb=" O LEU L 97 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG L 25 " pdb=" OD2 ASP L 71 " model vdw 2.288 3.120 nonbonded pdb=" OE2 GLU A 212 " pdb=" NZ LYS A 279 " model vdw 2.289 3.120 ... (remaining 33512 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=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: 0.500 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.840 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.006 0.047 4166 Z= 0.392 Angle : 0.865 11.946 5638 Z= 0.623 Chirality : 0.060 0.299 633 Planarity : 0.005 0.044 703 Dihedral : 14.935 87.656 1533 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.69 % Allowed : 3.67 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.92 (0.38), residues: 504 helix: 2.40 (0.31), residues: 258 sheet: -0.11 (0.50), residues: 109 loop : 0.38 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.026 0.001 TYR A 260 PHE 0.019 0.002 PHE A 151 TRP 0.024 0.002 TRP A 97 HIS 0.001 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 4162) covalent geometry : angle 0.86005 ( 5630) SS BOND : bond 0.00473 ( 4) SS BOND : angle 2.60761 ( 8) hydrogen bonds : bond 0.11213 ( 306) hydrogen bonds : angle 5.51932 ( 923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7253 (tppp) cc_final: 0.6452 (tmmt) REVERT: A 118 ASP cc_start: 0.7385 (m-30) cc_final: 0.7040 (m-30) REVERT: H 72 THR cc_start: 0.8438 (m) cc_final: 0.8232 (m) REVERT: H 85 GLN cc_start: 0.7999 (tp40) cc_final: 0.7499 (tp40) outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.4989 time to fit residues: 49.6167 Evaluate side-chains 69 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.177395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143522 restraints weight = 18518.718| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 8.01 r_work: 0.2944 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4166 Z= 0.158 Angle : 0.542 5.935 5638 Z= 0.289 Chirality : 0.038 0.137 633 Planarity : 0.004 0.037 703 Dihedral : 4.589 43.634 565 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.52 % Allowed : 14.91 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.62 (0.37), residues: 504 helix: 3.10 (0.29), residues: 263 sheet: 0.01 (0.50), residues: 106 loop : 0.48 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.012 0.001 TYR L 92 PHE 0.039 0.002 PHE L 84 TRP 0.014 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4162) covalent geometry : angle 0.53632 ( 5630) SS BOND : bond 0.00476 ( 4) SS BOND : angle 2.07386 ( 8) hydrogen bonds : bond 0.04476 ( 306) hydrogen bonds : angle 3.99103 ( 923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7242 (tppp) cc_final: 0.6391 (tmmt) REVERT: A 97 TRP cc_start: 0.7986 (t-100) cc_final: 0.7299 (t-100) REVERT: A 118 ASP cc_start: 0.7853 (m-30) cc_final: 0.7569 (m-30) REVERT: A 194 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7556 (mttt) REVERT: H 72 THR cc_start: 0.8247 (m) cc_final: 0.8046 (m) REVERT: H 85 GLN cc_start: 0.8024 (tp40) cc_final: 0.7462 (tp40) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.5152 time to fit residues: 41.0373 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.176855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118634 restraints weight = 15549.636| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.13 r_work: 0.3048 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4166 Z= 0.161 Angle : 0.529 6.490 5638 Z= 0.279 Chirality : 0.038 0.131 633 Planarity : 0.004 0.037 703 Dihedral : 4.549 41.513 563 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 16.51 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.72 (0.37), residues: 504 helix: 3.25 (0.29), residues: 263 sheet: -0.06 (0.50), residues: 106 loop : 0.50 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.044 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4162) covalent geometry : angle 0.52570 ( 5630) SS BOND : bond 0.00462 ( 4) SS BOND : angle 1.65395 ( 8) hydrogen bonds : bond 0.04364 ( 306) hydrogen bonds : angle 3.91825 ( 923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7281 (tppp) cc_final: 0.6452 (tmmt) REVERT: A 118 ASP cc_start: 0.7908 (m-30) cc_final: 0.7643 (m-30) REVERT: A 194 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7625 (mttt) REVERT: H 85 GLN cc_start: 0.8157 (tp40) cc_final: 0.7740 (tp40) REVERT: L 4 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (mp-120) outliers start: 12 outliers final: 4 residues processed: 77 average time/residue: 0.5230 time to fit residues: 41.7971 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.176710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116324 restraints weight = 13599.068| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.37 r_work: 0.3050 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4166 Z= 0.161 Angle : 0.529 6.490 5638 Z= 0.279 Chirality : 0.038 0.131 633 Planarity : 0.004 0.037 703 Dihedral : 4.549 41.513 563 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.38 % Allowed : 18.81 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.72 (0.37), residues: 504 helix: 3.25 (0.29), residues: 263 sheet: -0.06 (0.50), residues: 106 loop : 0.50 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.044 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4162) covalent geometry : angle 0.52570 ( 5630) SS BOND : bond 0.00462 ( 4) SS BOND : angle 1.65395 ( 8) hydrogen bonds : bond 0.04364 ( 306) hydrogen bonds : angle 3.91825 ( 923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7301 (tppp) cc_final: 0.6471 (tmmt) REVERT: A 118 ASP cc_start: 0.7942 (m-30) cc_final: 0.7684 (m-30) REVERT: A 194 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7650 (mttt) REVERT: H 85 GLN cc_start: 0.8135 (tp40) cc_final: 0.7759 (tp40) REVERT: L 4 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8253 (mp-120) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.5366 time to fit residues: 37.3243 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.179270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120972 restraints weight = 13853.618| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.29 r_work: 0.3153 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4166 Z= 0.152 Angle : 0.518 7.970 5638 Z= 0.273 Chirality : 0.038 0.146 633 Planarity : 0.004 0.037 703 Dihedral : 4.546 40.670 563 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.06 % Allowed : 18.81 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.82 (0.38), residues: 504 helix: 3.42 (0.28), residues: 257 sheet: -0.05 (0.51), residues: 106 loop : 0.50 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.047 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4162) covalent geometry : angle 0.51534 ( 5630) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.52309 ( 8) hydrogen bonds : bond 0.04258 ( 306) hydrogen bonds : angle 3.85495 ( 923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7211 (tppp) cc_final: 0.6339 (tmmt) REVERT: A 118 ASP cc_start: 0.7681 (m-30) cc_final: 0.7446 (m-30) REVERT: A 194 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7387 (mttt) REVERT: H 85 GLN cc_start: 0.7959 (tp40) cc_final: 0.7562 (tp40) REVERT: L 4 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8077 (mp-120) outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 0.5233 time to fit residues: 36.8779 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126053 restraints weight = 19375.065| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.69 r_work: 0.3206 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4166 Z= 0.152 Angle : 0.518 7.970 5638 Z= 0.273 Chirality : 0.038 0.146 633 Planarity : 0.004 0.037 703 Dihedral : 4.546 40.670 563 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.38 % Allowed : 19.50 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.82 (0.38), residues: 504 helix: 3.42 (0.28), residues: 257 sheet: -0.05 (0.51), residues: 106 loop : 0.50 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.047 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4162) covalent geometry : angle 0.51534 ( 5630) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.52313 ( 8) hydrogen bonds : bond 0.04258 ( 306) hydrogen bonds : angle 3.85495 ( 923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7296 (tppp) cc_final: 0.6439 (tmmt) REVERT: A 118 ASP cc_start: 0.7905 (m-30) cc_final: 0.7696 (m-30) REVERT: A 194 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7531 (mttt) REVERT: H 85 GLN cc_start: 0.8085 (tp40) cc_final: 0.7696 (tp40) REVERT: L 4 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8217 (mp-120) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.5345 time to fit residues: 39.3227 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.185141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127700 restraints weight = 14713.965| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.12 r_work: 0.3230 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4166 Z= 0.152 Angle : 0.518 7.967 5638 Z= 0.273 Chirality : 0.038 0.146 633 Planarity : 0.004 0.037 703 Dihedral : 4.552 40.670 563 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.38 % Allowed : 19.50 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.82 (0.38), residues: 504 helix: 3.42 (0.28), residues: 257 sheet: -0.05 (0.51), residues: 106 loop : 0.50 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.046 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4162) covalent geometry : angle 0.51524 ( 5630) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.52373 ( 8) hydrogen bonds : bond 0.04258 ( 306) hydrogen bonds : angle 3.85494 ( 923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7301 (tppp) cc_final: 0.6447 (tmmt) REVERT: A 118 ASP cc_start: 0.7890 (m-30) cc_final: 0.7683 (m-30) REVERT: A 194 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7528 (mttt) REVERT: H 85 GLN cc_start: 0.8097 (tp40) cc_final: 0.7713 (tp40) REVERT: L 4 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8185 (mp-120) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.4975 time to fit residues: 36.6788 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.185187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128194 restraints weight = 16091.879| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.64 r_work: 0.3209 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4166 Z= 0.152 Angle : 0.517 7.930 5638 Z= 0.272 Chirality : 0.038 0.143 633 Planarity : 0.004 0.037 703 Dihedral : 4.630 40.674 563 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.38 % Allowed : 19.50 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.82 (0.38), residues: 504 helix: 3.42 (0.28), residues: 257 sheet: -0.05 (0.51), residues: 106 loop : 0.50 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.011 0.001 TYR L 92 PHE 0.045 0.002 PHE L 84 TRP 0.008 0.002 TRP H 117 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4162) covalent geometry : angle 0.51393 ( 5630) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.53285 ( 8) hydrogen bonds : bond 0.04258 ( 306) hydrogen bonds : angle 3.85481 ( 923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7307 (tppp) cc_final: 0.6451 (tmmt) REVERT: A 118 ASP cc_start: 0.7896 (m-30) cc_final: 0.7684 (m-30) REVERT: A 194 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7533 (mttt) REVERT: H 85 GLN cc_start: 0.8095 (tp40) cc_final: 0.7708 (tp40) REVERT: L 4 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8198 (mp-120) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.5137 time to fit residues: 37.8814 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain L residue 4 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121414 restraints weight = 13928.545| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.36 r_work: 0.3133 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4166 Z= 0.139 Angle : 0.535 9.428 5638 Z= 0.278 Chirality : 0.038 0.131 633 Planarity : 0.004 0.037 703 Dihedral : 4.542 39.823 563 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 18.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.89 (0.38), residues: 504 helix: 3.49 (0.29), residues: 257 sheet: -0.00 (0.51), residues: 106 loop : 0.49 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.010 0.001 TYR L 92 PHE 0.051 0.002 PHE L 84 TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4162) covalent geometry : angle 0.53186 ( 5630) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.60624 ( 8) hydrogen bonds : bond 0.04156 ( 306) hydrogen bonds : angle 3.78294 ( 923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7084 (tppp) cc_final: 0.6226 (tmmt) REVERT: A 118 ASP cc_start: 0.7593 (m-30) cc_final: 0.7340 (m-30) REVERT: A 194 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7304 (mttt) REVERT: H 85 GLN cc_start: 0.7826 (tp40) cc_final: 0.7511 (tp40) REVERT: H 87 ASN cc_start: 0.7637 (m-40) cc_final: 0.7431 (m110) REVERT: L 4 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8001 (mp-120) REVERT: L 82 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7892 (pm20) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.4680 time to fit residues: 35.4130 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.179838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119427 restraints weight = 17681.236| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.60 r_work: 0.3178 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4166 Z= 0.139 Angle : 0.535 9.426 5638 Z= 0.278 Chirality : 0.038 0.131 633 Planarity : 0.004 0.037 703 Dihedral : 4.542 39.823 563 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.61 % Allowed : 19.27 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.89 (0.38), residues: 504 helix: 3.49 (0.29), residues: 257 sheet: -0.00 (0.51), residues: 106 loop : 0.49 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.010 0.001 TYR L 92 PHE 0.051 0.002 PHE L 84 TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4162) covalent geometry : angle 0.53179 ( 5630) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.60626 ( 8) hydrogen bonds : bond 0.04156 ( 306) hydrogen bonds : angle 3.78295 ( 923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7089 (tppp) cc_final: 0.6230 (tmmt) REVERT: A 118 ASP cc_start: 0.7525 (m-30) cc_final: 0.7266 (m-30) REVERT: A 194 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7292 (mttt) REVERT: H 85 GLN cc_start: 0.7813 (tp40) cc_final: 0.7496 (tp40) REVERT: H 87 ASN cc_start: 0.7640 (m-40) cc_final: 0.7434 (m110) REVERT: L 4 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7981 (mp-120) REVERT: L 82 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7879 (pm20) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.5198 time to fit residues: 35.0792 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.179838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119062 restraints weight = 19101.965| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.80 r_work: 0.3119 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4166 Z= 0.139 Angle : 0.535 9.426 5638 Z= 0.278 Chirality : 0.038 0.131 633 Planarity : 0.004 0.037 703 Dihedral : 4.542 39.823 563 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.61 % Allowed : 19.27 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.89 (0.38), residues: 504 helix: 3.49 (0.29), residues: 257 sheet: -0.00 (0.51), residues: 106 loop : 0.49 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.010 0.001 TYR L 92 PHE 0.051 0.002 PHE L 84 TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4162) covalent geometry : angle 0.53179 ( 5630) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.60626 ( 8) hydrogen bonds : bond 0.04156 ( 306) hydrogen bonds : angle 3.78295 ( 923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.71 seconds wall clock time: 34 minutes 7.77 seconds (2047.77 seconds total)