Starting phenix.real_space_refine on Tue Mar 11 17:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.map" model { file = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2025/7stf_25427.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4030 2.51 5 N 1104 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6414 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 62 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1663 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Time building chain proxies: 4.87, per 1000 atoms: 0.76 Number of scatterers: 6414 At special positions: 0 Unit cell: (70.052, 64.144, 145.168, 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 23 16.00 O 1257 8.00 N 1104 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 12.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.652A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.861A pdb=" N TYR L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.616A pdb=" N GLN A 54 " --> pdb=" O TRP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.633A pdb=" N THR A 228 " --> pdb=" O THR A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.654A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.749A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.865A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.786A pdb=" N THR L 74 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.910A pdb=" N PHE L 118 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU L 137 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE L 120 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.755A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 168 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.959A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB4, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB5, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.624A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.777A pdb=" N PHE B 90 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.713A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 417 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: 1.91 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2076 1.34 - 1.47: 1710 1.47 - 1.59: 2755 1.59 - 1.72: 0 1.72 - 1.85: 32 Bond restraints: 6573 Sorted by residual: bond pdb=" C ARG H 98 " pdb=" N ALA H 99 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.97e-02 2.58e+03 9.41e+00 bond pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " ideal model delta sigma weight residual 1.534 1.488 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.27e-02 6.20e+03 5.53e+00 ... (remaining 6568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 8668 3.09 - 6.18: 230 6.18 - 9.26: 31 9.26 - 12.35: 4 12.35 - 15.44: 2 Bond angle restraints: 8935 Sorted by residual: angle pdb=" C PHE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.80 106.36 15.44 2.44e+00 1.68e-01 4.00e+01 angle pdb=" C SER L 52 " pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 121.72 131.19 -9.47 1.54e+00 4.22e-01 3.78e+01 angle pdb=" C GLN L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta sigma weight residual 121.54 132.85 -11.31 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.42 113.90 8.52 1.55e+00 4.16e-01 3.02e+01 angle pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" C TYR L 92 " ideal model delta sigma weight residual 110.80 122.19 -11.39 2.13e+00 2.20e-01 2.86e+01 ... (remaining 8930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3403 16.18 - 32.36: 405 32.36 - 48.53: 79 48.53 - 64.71: 15 64.71 - 80.89: 15 Dihedral angle restraints: 3917 sinusoidal: 1545 harmonic: 2372 Sorted by residual: dihedral pdb=" CA SER L 91 " pdb=" C SER L 91 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " ideal model delta harmonic sigma weight residual -180.00 -124.10 -55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASP A 29 " pdb=" C ASP A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA ASN H 77 " pdb=" C ASN H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta harmonic sigma weight residual -180.00 -140.14 -39.86 0 5.00e+00 4.00e-02 6.36e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 882 0.105 - 0.209: 82 0.209 - 0.314: 1 0.314 - 0.418: 1 0.418 - 0.523: 1 Chirality restraints: 967 Sorted by residual: chirality pdb=" CG LEU L 46 " pdb=" CB LEU L 46 " pdb=" CD1 LEU L 46 " pdb=" CD2 LEU L 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA MET H 52 " pdb=" N MET H 52 " pdb=" C MET H 52 " pdb=" CB MET H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 964 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 125 " -0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO H 126 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU A 160 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 161 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 109 " 0.031 2.00e-02 2.50e+03 2.12e-02 8.98e+00 pdb=" CG TYR H 109 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR H 109 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 109 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 109 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 134 2.58 - 3.16: 6039 3.16 - 3.74: 10420 3.74 - 4.32: 14730 4.32 - 4.90: 23459 Nonbonded interactions: 54782 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O ASP L 70 " model vdw 1.998 3.120 nonbonded pdb=" OG SER B 31 " pdb=" O HIS B 33 " model vdw 2.054 3.040 nonbonded pdb=" O HIS H 208 " pdb=" OG SER H 211 " model vdw 2.115 3.040 nonbonded pdb=" OG SER H 75 " pdb=" OD1 ASN H 77 " model vdw 2.120 3.040 nonbonded pdb=" O VAL H 2 " pdb=" ND2 ASN H 101 " model vdw 2.164 3.120 ... (remaining 54777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.009 0.085 6573 Z= 0.599 Angle : 1.206 15.438 8935 Z= 0.665 Chirality : 0.062 0.523 967 Planarity : 0.007 0.093 1161 Dihedral : 15.262 80.889 2376 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 20.12 % Favored : 79.13 % Rotamer: Outliers : 0.14 % Allowed : 0.85 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 1.04 % 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: -3.76 (0.27), residues: 805 helix: -1.22 (0.53), residues: 87 sheet: -1.69 (0.34), residues: 211 loop : -3.30 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 162 HIS 0.012 0.003 HIS H 57 PHE 0.044 0.004 PHE L 95 TYR 0.050 0.005 TYR H 109 ARG 0.013 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.7543 (m170) cc_final: 0.7150 (m-70) REVERT: B 39 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7345 (mptt) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2805 time to fit residues: 34.6810 Evaluate side-chains 72 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.140676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.106954 restraints weight = 13390.586| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.03 r_work: 0.3882 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.286 Angle : 0.913 10.607 8935 Z= 0.485 Chirality : 0.051 0.201 967 Planarity : 0.006 0.059 1161 Dihedral : 8.448 69.716 896 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.90 % Favored : 83.85 % Rotamer: Outliers : 0.85 % Allowed : 10.10 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.65 % 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: -3.59 (0.28), residues: 805 helix: -0.67 (0.55), residues: 97 sheet: -1.66 (0.33), residues: 226 loop : -3.29 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 204 HIS 0.011 0.002 HIS B 51 PHE 0.030 0.003 PHE L 95 TYR 0.024 0.002 TYR L 49 ARG 0.006 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7153 (p0) cc_final: 0.6372 (m-30) REVERT: H 98 ARG cc_start: 0.6986 (tpp-160) cc_final: 0.6623 (mtt-85) REVERT: H 110 TRP cc_start: 0.5092 (p90) cc_final: 0.4328 (p90) REVERT: H 153 TYR cc_start: 0.6322 (p90) cc_final: 0.5545 (p90) REVERT: H 163 ASN cc_start: 0.7275 (t0) cc_final: 0.6991 (m-40) REVERT: L 55 TYR cc_start: 0.6345 (t80) cc_final: 0.6123 (t80) REVERT: A 108 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6959 (tpt170) REVERT: B 36 GLU cc_start: 0.6653 (tp30) cc_final: 0.6296 (tp30) REVERT: B 37 ASN cc_start: 0.7841 (m110) cc_final: 0.7389 (m-40) REVERT: B 118 ASP cc_start: 0.7901 (t0) cc_final: 0.7690 (t0) outliers start: 6 outliers final: 6 residues processed: 96 average time/residue: 0.2330 time to fit residues: 29.2528 Evaluate side-chains 77 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 31 optimal weight: 0.0570 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.140452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.106521 restraints weight = 13451.523| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.01 r_work: 0.3872 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6573 Z= 0.277 Angle : 0.850 10.694 8935 Z= 0.449 Chirality : 0.049 0.199 967 Planarity : 0.006 0.060 1161 Dihedral : 7.986 65.621 896 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.78 % Favored : 83.98 % Rotamer: Outliers : 2.70 % Allowed : 14.65 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.45 (0.28), residues: 805 helix: -0.52 (0.55), residues: 96 sheet: -1.49 (0.35), residues: 211 loop : -3.22 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 PHE 0.014 0.002 PHE H 129 TYR 0.024 0.002 TYR L 49 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5687 (t80) REVERT: H 73 ASP cc_start: 0.7239 (p0) cc_final: 0.6523 (m-30) REVERT: H 93 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8480 (m) REVERT: H 110 TRP cc_start: 0.4847 (p90) cc_final: 0.4413 (p90) REVERT: H 153 TYR cc_start: 0.6470 (p90) cc_final: 0.5656 (p90) REVERT: H 163 ASN cc_start: 0.7029 (t0) cc_final: 0.6808 (m-40) REVERT: B 36 GLU cc_start: 0.6651 (tp30) cc_final: 0.6382 (tp30) REVERT: B 37 ASN cc_start: 0.7909 (m110) cc_final: 0.7432 (m-40) REVERT: B 116 ASP cc_start: 0.8253 (t0) cc_final: 0.7979 (t0) outliers start: 19 outliers final: 11 residues processed: 92 average time/residue: 0.2053 time to fit residues: 24.9362 Evaluate side-chains 79 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 8 optimal weight: 0.0070 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.144178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.110811 restraints weight = 13524.533| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.08 r_work: 0.3958 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6573 Z= 0.209 Angle : 0.789 10.403 8935 Z= 0.413 Chirality : 0.047 0.203 967 Planarity : 0.006 0.057 1161 Dihedral : 7.461 57.841 896 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.91 % Favored : 85.84 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.25 (0.29), residues: 805 helix: -0.34 (0.56), residues: 95 sheet: -1.48 (0.34), residues: 227 loop : -3.05 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 204 HIS 0.007 0.001 HIS B 51 PHE 0.015 0.001 PHE H 129 TYR 0.018 0.002 TYR L 49 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: H 73 ASP cc_start: 0.6938 (p0) cc_final: 0.6659 (m-30) REVERT: H 77 ASN cc_start: 0.6923 (m110) cc_final: 0.6549 (t0) REVERT: H 98 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6649 (mtm110) REVERT: H 153 TYR cc_start: 0.6555 (p90) cc_final: 0.5764 (p90) REVERT: H 163 ASN cc_start: 0.7066 (t0) cc_final: 0.6846 (m-40) REVERT: L 141 PHE cc_start: 0.6347 (p90) cc_final: 0.6128 (p90) REVERT: A 108 ARG cc_start: 0.7144 (tpt170) cc_final: 0.6884 (tpt170) REVERT: B 37 ASN cc_start: 0.7776 (m110) cc_final: 0.7363 (m-40) REVERT: B 112 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 116 ASP cc_start: 0.8259 (t0) cc_final: 0.7911 (t0) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.2009 time to fit residues: 25.0982 Evaluate side-chains 90 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.140053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.105503 restraints weight = 13357.245| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.10 r_work: 0.3844 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6573 Z= 0.324 Angle : 0.834 10.590 8935 Z= 0.441 Chirality : 0.049 0.248 967 Planarity : 0.006 0.056 1161 Dihedral : 7.614 58.270 896 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.40 % Favored : 83.35 % Rotamer: Outliers : 3.98 % Allowed : 16.93 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.46 (0.28), residues: 805 helix: -0.57 (0.53), residues: 102 sheet: -1.48 (0.34), residues: 227 loop : -3.29 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 204 HIS 0.009 0.002 HIS B 51 PHE 0.015 0.002 PHE H 129 TYR 0.031 0.003 TYR L 49 ARG 0.004 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5459 (t80) REVERT: H 73 ASP cc_start: 0.7390 (p0) cc_final: 0.6730 (m-30) REVERT: H 77 ASN cc_start: 0.7394 (m110) cc_final: 0.6748 (t0) REVERT: H 98 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6741 (mtm-85) REVERT: H 105 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6299 (t80) REVERT: H 153 TYR cc_start: 0.6685 (p90) cc_final: 0.5834 (p90) REVERT: B 36 GLU cc_start: 0.6367 (tp30) cc_final: 0.5919 (tp30) REVERT: B 39 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7945 (mmtm) REVERT: B 112 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 116 ASP cc_start: 0.8399 (t0) cc_final: 0.8068 (t0) outliers start: 28 outliers final: 20 residues processed: 93 average time/residue: 0.1868 time to fit residues: 23.3969 Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 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 = 0.4568 r_free = 0.4568 target = 0.143190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.109194 restraints weight = 13428.200| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.14 r_work: 0.3916 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6573 Z= 0.223 Angle : 0.781 10.274 8935 Z= 0.407 Chirality : 0.047 0.194 967 Planarity : 0.006 0.075 1161 Dihedral : 7.275 53.483 896 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.29 % Favored : 85.47 % Rotamer: Outliers : 4.13 % Allowed : 18.35 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.40 (0.28), residues: 805 helix: -0.34 (0.54), residues: 100 sheet: -1.34 (0.35), residues: 207 loop : -3.28 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.008 0.001 HIS B 51 PHE 0.013 0.001 PHE H 129 TYR 0.021 0.002 TYR H 95 ARG 0.005 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.5387 (t80) REVERT: H 35 HIS cc_start: 0.7806 (m-70) cc_final: 0.7603 (m90) REVERT: H 73 ASP cc_start: 0.7044 (p0) cc_final: 0.6648 (m-30) REVERT: H 105 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5806 (t80) REVERT: H 153 TYR cc_start: 0.6621 (p90) cc_final: 0.5744 (p90) REVERT: A 108 ARG cc_start: 0.7024 (tpt170) cc_final: 0.6725 (tpt170) REVERT: B 36 GLU cc_start: 0.6373 (tp30) cc_final: 0.6067 (tp30) REVERT: B 112 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 116 ASP cc_start: 0.8350 (t0) cc_final: 0.7991 (t0) outliers start: 29 outliers final: 18 residues processed: 97 average time/residue: 0.1981 time to fit residues: 25.9249 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.138438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.104011 restraints weight = 13319.909| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.00 r_work: 0.3819 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6573 Z= 0.406 Angle : 0.880 10.759 8935 Z= 0.465 Chirality : 0.050 0.272 967 Planarity : 0.008 0.137 1161 Dihedral : 7.780 62.023 896 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.76 % Favored : 81.99 % Rotamer: Outliers : 3.98 % Allowed : 19.49 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.53 (0.27), residues: 805 helix: -0.49 (0.54), residues: 101 sheet: -1.25 (0.34), residues: 214 loop : -3.49 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 110 HIS 0.010 0.002 HIS B 51 PHE 0.034 0.003 PHE L 141 TYR 0.035 0.003 TYR L 49 ARG 0.010 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5457 (t80) REVERT: H 35 HIS cc_start: 0.8024 (m-70) cc_final: 0.7768 (m90) REVERT: H 77 ASN cc_start: 0.7420 (m110) cc_final: 0.6751 (t0) REVERT: H 105 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6038 (t80) REVERT: H 153 TYR cc_start: 0.6682 (p90) cc_final: 0.5768 (p90) REVERT: A 108 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6848 (tpt170) REVERT: B 36 GLU cc_start: 0.6453 (tp30) cc_final: 0.6055 (tp30) REVERT: B 39 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7859 (mmtm) REVERT: B 116 ASP cc_start: 0.8492 (t0) cc_final: 0.8156 (t0) outliers start: 28 outliers final: 21 residues processed: 91 average time/residue: 0.1783 time to fit residues: 21.9939 Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 140 ASN A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.139699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.105330 restraints weight = 13351.351| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.03 r_work: 0.3849 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6573 Z= 0.328 Angle : 0.848 10.530 8935 Z= 0.444 Chirality : 0.050 0.252 967 Planarity : 0.007 0.102 1161 Dihedral : 7.698 61.372 896 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.78 % Favored : 83.98 % Rotamer: Outliers : 3.70 % Allowed : 20.48 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.59 (0.27), residues: 805 helix: -0.46 (0.54), residues: 101 sheet: -1.43 (0.33), residues: 220 loop : -3.48 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 110 HIS 0.009 0.002 HIS B 51 PHE 0.026 0.002 PHE L 141 TYR 0.025 0.003 TYR L 49 ARG 0.010 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.762 Fit side-chains REVERT: H 31 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5576 (t80) REVERT: H 35 HIS cc_start: 0.7984 (m-70) cc_final: 0.7708 (m90) REVERT: H 73 ASP cc_start: 0.7498 (p0) cc_final: 0.6755 (m-30) REVERT: H 77 ASN cc_start: 0.7411 (m110) cc_final: 0.6726 (t0) REVERT: H 105 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.5910 (t80) REVERT: H 153 TYR cc_start: 0.6681 (p90) cc_final: 0.5786 (p90) REVERT: A 108 ARG cc_start: 0.7164 (tpt170) cc_final: 0.6907 (tpt170) REVERT: A 204 TRP cc_start: 0.7426 (m100) cc_final: 0.7196 (m100) REVERT: B 36 GLU cc_start: 0.6540 (tp30) cc_final: 0.6135 (tp30) REVERT: B 39 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7872 (mmtm) REVERT: B 116 ASP cc_start: 0.8450 (t0) cc_final: 0.8114 (t0) outliers start: 26 outliers final: 20 residues processed: 91 average time/residue: 0.1846 time to fit residues: 22.7208 Evaluate side-chains 94 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.106539 restraints weight = 13444.461| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.08 r_work: 0.3868 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6573 Z= 0.274 Angle : 0.818 10.188 8935 Z= 0.426 Chirality : 0.048 0.243 967 Planarity : 0.006 0.075 1161 Dihedral : 7.450 57.574 896 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.27 % Favored : 83.48 % Rotamer: Outliers : 3.27 % Allowed : 21.05 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.52 (0.27), residues: 805 helix: -0.30 (0.55), residues: 100 sheet: -1.45 (0.33), residues: 226 loop : -3.44 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 PHE 0.021 0.002 PHE L 141 TYR 0.021 0.002 TYR H 184 ARG 0.009 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5531 (t80) REVERT: H 35 HIS cc_start: 0.7868 (m-70) cc_final: 0.7627 (m90) REVERT: H 73 ASP cc_start: 0.7396 (p0) cc_final: 0.6742 (m-30) REVERT: H 77 ASN cc_start: 0.7391 (m110) cc_final: 0.6850 (t0) REVERT: H 105 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.5833 (t80) REVERT: H 153 TYR cc_start: 0.6674 (p90) cc_final: 0.5749 (p90) REVERT: A 204 TRP cc_start: 0.7450 (m100) cc_final: 0.7195 (m100) REVERT: B 36 GLU cc_start: 0.6442 (tp30) cc_final: 0.6134 (tp30) REVERT: B 116 ASP cc_start: 0.8419 (t0) cc_final: 0.8086 (t0) outliers start: 23 outliers final: 19 residues processed: 93 average time/residue: 0.1890 time to fit residues: 23.8403 Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.143308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.111048 restraints weight = 13532.499| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.56 r_work: 0.3902 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6573 Z= 0.229 Angle : 0.794 9.932 8935 Z= 0.412 Chirality : 0.047 0.232 967 Planarity : 0.008 0.189 1161 Dihedral : 7.229 51.372 896 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.16 % Favored : 85.59 % Rotamer: Outliers : 2.99 % Allowed : 21.62 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.44 (0.28), residues: 805 helix: -0.25 (0.54), residues: 100 sheet: -1.56 (0.31), residues: 255 loop : -3.36 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 36 HIS 0.008 0.001 HIS B 51 PHE 0.018 0.002 PHE L 141 TYR 0.019 0.002 TYR H 184 ARG 0.007 0.000 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5475 (t80) REVERT: H 73 ASP cc_start: 0.7108 (p0) cc_final: 0.6717 (m-30) REVERT: H 77 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6748 (t0) REVERT: H 82 GLN cc_start: 0.7368 (tm-30) cc_final: 0.6692 (tm-30) REVERT: H 105 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.5705 (t80) REVERT: H 153 TYR cc_start: 0.6702 (p90) cc_final: 0.5801 (p90) REVERT: C 16 LYS cc_start: 0.7566 (ttmm) cc_final: 0.7299 (ttmm) REVERT: L 47 LEU cc_start: 0.7587 (mp) cc_final: 0.7333 (mt) REVERT: A 204 TRP cc_start: 0.7456 (m100) cc_final: 0.7249 (m100) REVERT: B 36 GLU cc_start: 0.6432 (tp30) cc_final: 0.6217 (tp30) REVERT: B 116 ASP cc_start: 0.8362 (t0) cc_final: 0.8019 (t0) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.2008 time to fit residues: 24.7932 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.142618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.109977 restraints weight = 13587.726| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.50 r_work: 0.3890 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.297 6573 Z= 0.431 Angle : 1.195 59.179 8935 Z= 0.688 Chirality : 0.050 0.316 967 Planarity : 0.008 0.174 1161 Dihedral : 7.338 51.337 896 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.16 % Favored : 85.59 % Rotamer: Outliers : 2.99 % Allowed : 22.19 % Favored : 74.82 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.43 (0.28), residues: 805 helix: -0.23 (0.54), residues: 100 sheet: -1.56 (0.31), residues: 255 loop : -3.35 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 36 HIS 0.024 0.002 HIS A 151 PHE 0.015 0.002 PHE L 141 TYR 0.017 0.002 TYR H 184 ARG 0.025 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4474.96 seconds wall clock time: 77 minutes 23.38 seconds (4643.38 seconds total)