Starting phenix.real_space_refine on Mon Jan 13 19:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.map" model { file = "/net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r47_18881/01_2025/8r47_18881.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2376 2.51 5 N 636 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.73, per 1000 atoms: 0.46 Number of scatterers: 3780 At special positions: 0 Unit cell: (77.522, 81.258, 45.766, 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 12 16.00 O 756 8.00 N 636 7.00 C 2376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " 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=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 477.9 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.776A pdb=" N CYS B 22 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS C 22 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS D 22 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 22 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS F 22 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.803A pdb=" N LEU A 27 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 28 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 28 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 28 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 28 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG F 28 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.409A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR E 35 " --> pdb=" O GLN F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.591A pdb=" N LEU A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 44 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE C 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL B 46 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE D 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 44 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 46 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 44 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE F 47 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 46 " --> pdb=" O ILE F 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.542A pdb=" N ALA A 70 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 70 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR C 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 70 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR D 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 72 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 70 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 70 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR F 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 72 " --> pdb=" O THR F 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 105 60 hydrogen bonds defined for protein. 180 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: 0.91 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 648 1.31 - 1.44: 1116 1.44 - 1.57: 2082 1.57 - 1.69: 0 1.69 - 1.82: 12 Bond restraints: 3858 Sorted by residual: bond pdb=" C GLN F 16 " pdb=" O GLN F 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN A 16 " pdb=" O GLN A 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN C 16 " pdb=" O GLN C 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN D 16 " pdb=" O GLN D 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN B 16 " pdb=" O GLN B 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.24e+01 ... (remaining 3853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 3849 1.97 - 3.94: 989 3.94 - 5.91: 328 5.91 - 7.88: 54 7.88 - 9.85: 18 Bond angle restraints: 5238 Sorted by residual: angle pdb=" CA GLY E 94 " pdb=" C GLY E 94 " pdb=" O GLY E 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY C 94 " pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY F 94 " pdb=" C GLY F 94 " pdb=" O GLY F 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY A 94 " pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 121.04 115.89 5.15 7.90e-01 1.60e+00 4.24e+01 angle pdb=" CA GLY D 94 " pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 121.04 115.90 5.14 7.90e-01 1.60e+00 4.23e+01 ... (remaining 5233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1921 16.00 - 32.00: 200 32.00 - 48.00: 42 48.00 - 64.00: 24 64.00 - 80.00: 6 Dihedral angle restraints: 2193 sinusoidal: 813 harmonic: 1380 Sorted by residual: dihedral pdb=" CA PRO D 39 " pdb=" C PRO D 39 " pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO F 39 " pdb=" C PRO F 39 " pdb=" N GLY F 40 " pdb=" CA GLY F 40 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 399 0.083 - 0.165: 135 0.165 - 0.248: 30 0.248 - 0.330: 6 0.330 - 0.413: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA ILE F 65 " pdb=" N ILE F 65 " pdb=" C ILE F 65 " pdb=" CB ILE F 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 573 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 63 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLY B 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY B 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER B 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY A 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY A 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER A 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY D 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY D 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER D 64 " 0.029 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 45 2.61 - 3.18: 3074 3.18 - 3.76: 6106 3.76 - 4.33: 9435 4.33 - 4.90: 17013 Nonbonded interactions: 35673 Sorted by model distance: nonbonded pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " model vdw 2.042 3.760 ... (remaining 35668 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.920 Find NCS groups from input model: 0.070 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.013 0.054 3858 Z= 0.842 Angle : 2.036 9.847 5238 Z= 1.468 Chirality : 0.097 0.413 576 Planarity : 0.016 0.070 672 Dihedral : 15.668 79.999 1326 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.21), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 97 PHE 0.008 0.001 PHE C 61 TYR 0.004 0.001 TYR C 30 ARG 0.002 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.413 Fit side-chains REVERT: B 66 SER cc_start: 0.8301 (p) cc_final: 0.8059 (t) REVERT: D 90 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6716 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.5412 time to fit residues: 43.3632 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 23 GLN E 23 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.150189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.131742 restraints weight = 3933.390| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.41 r_work: 0.3861 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3858 Z= 0.177 Angle : 0.606 8.378 5238 Z= 0.313 Chirality : 0.043 0.148 576 Planarity : 0.005 0.052 672 Dihedral : 5.883 14.817 534 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.76 % Allowed : 17.17 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.25), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 97 PHE 0.006 0.001 PHE D 61 TYR 0.010 0.001 TYR B 48 ARG 0.004 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.405 Fit side-chains REVERT: B 82 GLU cc_start: 0.8185 (tp30) cc_final: 0.7929 (mm-30) REVERT: C 82 GLU cc_start: 0.8173 (tp30) cc_final: 0.7900 (mm-30) REVERT: E 90 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7137 (mtt90) REVERT: F 66 SER cc_start: 0.8396 (p) cc_final: 0.8178 (p) REVERT: F 69 THR cc_start: 0.8213 (m) cc_final: 0.7815 (t) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.6599 time to fit residues: 55.2341 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN C 16 GLN F 16 GLN F 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.118841 restraints weight = 3961.399| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.40 r_work: 0.3709 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3858 Z= 0.483 Angle : 0.817 7.669 5238 Z= 0.425 Chirality : 0.052 0.174 576 Planarity : 0.006 0.050 672 Dihedral : 6.928 17.219 534 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.28 % Allowed : 16.16 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 97 PHE 0.011 0.002 PHE F 99 TYR 0.016 0.003 TYR A 48 ARG 0.010 0.002 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.405 Fit side-chains REVERT: D 69 THR cc_start: 0.8402 (m) cc_final: 0.8097 (t) REVERT: E 80 GLU cc_start: 0.7608 (tt0) cc_final: 0.7204 (tt0) REVERT: F 69 THR cc_start: 0.8303 (m) cc_final: 0.8027 (t) outliers start: 13 outliers final: 6 residues processed: 75 average time/residue: 0.8135 time to fit residues: 63.9082 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.148882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.131758 restraints weight = 3902.846| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.38 r_work: 0.3847 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3858 Z= 0.144 Angle : 0.570 7.999 5238 Z= 0.293 Chirality : 0.043 0.147 576 Planarity : 0.004 0.047 672 Dihedral : 5.896 18.514 534 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.26 % Allowed : 17.93 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.010 0.001 TYR C 48 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.433 Fit side-chains REVERT: C 90 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7082 (mmm160) REVERT: D 69 THR cc_start: 0.8389 (m) cc_final: 0.8038 (t) REVERT: F 69 THR cc_start: 0.8290 (m) cc_final: 0.7990 (t) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.7999 time to fit residues: 59.6137 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 23 optimal weight: 7.9990 overall best weight: 3.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.119934 restraints weight = 4047.171| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.41 r_work: 0.3723 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3858 Z= 0.419 Angle : 0.765 6.949 5238 Z= 0.402 Chirality : 0.051 0.178 576 Planarity : 0.005 0.052 672 Dihedral : 6.878 21.668 534 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.78 % Allowed : 15.66 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 97 PHE 0.009 0.002 PHE D 86 TYR 0.013 0.002 TYR D 48 ARG 0.008 0.002 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.423 Fit side-chains REVERT: C 80 GLU cc_start: 0.7690 (tt0) cc_final: 0.7401 (tm-30) REVERT: D 69 THR cc_start: 0.8440 (m) cc_final: 0.8103 (t) REVERT: F 69 THR cc_start: 0.8376 (m) cc_final: 0.8096 (t) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.8900 time to fit residues: 65.1936 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128478 restraints weight = 3952.137| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.41 r_work: 0.3807 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3858 Z= 0.170 Angle : 0.577 5.943 5238 Z= 0.302 Chirality : 0.044 0.147 576 Planarity : 0.005 0.050 672 Dihedral : 6.080 17.776 534 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.011 0.001 TYR A 48 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.436 Fit side-chains REVERT: C 80 GLU cc_start: 0.7550 (tt0) cc_final: 0.7241 (tm-30) REVERT: C 90 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7202 (mmm160) REVERT: D 69 THR cc_start: 0.8379 (m) cc_final: 0.8012 (t) REVERT: F 69 THR cc_start: 0.8311 (m) cc_final: 0.8010 (t) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.8689 time to fit residues: 62.7121 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.0370 overall best weight: 0.9270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128243 restraints weight = 3959.573| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.40 r_work: 0.3807 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3858 Z= 0.174 Angle : 0.593 7.334 5238 Z= 0.304 Chirality : 0.043 0.145 576 Planarity : 0.005 0.050 672 Dihedral : 5.981 17.164 534 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.76 % Allowed : 18.69 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.006 0.001 TYR E 85 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.458 Fit side-chains REVERT: C 80 GLU cc_start: 0.7469 (tt0) cc_final: 0.7160 (tm-30) REVERT: C 90 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7398 (mtp85) REVERT: D 69 THR cc_start: 0.8383 (m) cc_final: 0.8002 (t) REVERT: F 69 THR cc_start: 0.8290 (m) cc_final: 0.7981 (t) REVERT: F 103 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8031 (m) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.8862 time to fit residues: 58.5132 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.122480 restraints weight = 3946.790| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.39 r_work: 0.3749 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3858 Z= 0.267 Angle : 0.661 8.410 5238 Z= 0.345 Chirality : 0.046 0.155 576 Planarity : 0.005 0.051 672 Dihedral : 6.415 19.058 534 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.26 % Allowed : 18.18 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 97 PHE 0.007 0.002 PHE B 99 TYR 0.013 0.001 TYR D 48 ARG 0.004 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.429 Fit side-chains REVERT: C 80 GLU cc_start: 0.7576 (tt0) cc_final: 0.7269 (tm-30) REVERT: C 90 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7390 (mtp85) REVERT: D 69 THR cc_start: 0.8441 (m) cc_final: 0.8080 (t) REVERT: E 103 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8109 (m) REVERT: F 69 THR cc_start: 0.8379 (m) cc_final: 0.8067 (t) REVERT: F 103 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8057 (m) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.9024 time to fit residues: 60.2892 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.144856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127424 restraints weight = 3934.829| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.39 r_work: 0.3796 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3858 Z= 0.194 Angle : 0.615 8.307 5238 Z= 0.316 Chirality : 0.044 0.146 576 Planarity : 0.005 0.051 672 Dihedral : 6.111 17.270 534 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.52 % Allowed : 19.19 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.012 0.001 TYR D 48 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.488 Fit side-chains REVERT: C 80 GLU cc_start: 0.7492 (tt0) cc_final: 0.7184 (tm-30) REVERT: C 90 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7336 (mtp85) REVERT: E 103 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8119 (m) REVERT: F 69 THR cc_start: 0.8361 (m) cc_final: 0.8064 (t) REVERT: F 103 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8042 (m) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.8953 time to fit residues: 60.8844 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.133875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116221 restraints weight = 4051.558| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.41 r_work: 0.3676 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.060 3858 Z= 0.685 Angle : 0.986 10.889 5238 Z= 0.513 Chirality : 0.060 0.214 576 Planarity : 0.006 0.056 672 Dihedral : 7.409 21.469 534 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.77 % Allowed : 19.19 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 97 PHE 0.012 0.003 PHE A 61 TYR 0.018 0.003 TYR A 48 ARG 0.014 0.003 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.472 Fit side-chains REVERT: C 80 GLU cc_start: 0.7787 (tt0) cc_final: 0.7467 (tm-30) REVERT: C 90 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7478 (mtp85) REVERT: D 69 THR cc_start: 0.8446 (m) cc_final: 0.8142 (t) REVERT: F 69 THR cc_start: 0.8397 (m) cc_final: 0.8141 (t) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.9099 time to fit residues: 66.5173 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.128203 restraints weight = 3949.781| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.39 r_work: 0.3806 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3858 Z= 0.170 Angle : 0.629 8.737 5238 Z= 0.318 Chirality : 0.044 0.176 576 Planarity : 0.005 0.052 672 Dihedral : 6.175 16.818 534 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 19.95 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 97 PHE 0.007 0.001 PHE B 99 TYR 0.013 0.001 TYR D 48 ARG 0.002 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.82 seconds wall clock time: 55 minutes 20.69 seconds (3320.69 seconds total)