Starting phenix.real_space_refine on Thu Mar 6 05:10:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.map" model { file = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7b_23709/03_2025/7m7b_23709.cif" } resolution = 2.95 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= 0.001 sd= 0.056 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 17 5.16 5 C 3103 2.51 5 N 820 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain: "L" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1591 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.36, per 1000 atoms: 0.89 Number of scatterers: 4898 At special positions: 0 Unit cell: (105.692, 91.4418, 104.505, 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 17 16.00 O 958 8.00 N 820 7.00 C 3103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.02 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 633.5 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 12.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.833A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.674A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.764A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.594A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.753A pdb=" N ILE H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.541A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 152 203 hydrogen bonds defined for protein. 486 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: 1.58 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1318 1.33 - 1.46: 990 1.46 - 1.58: 2703 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 5029 Sorted by residual: bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" CZ ARG H 98 " pdb=" NH2 ARG H 98 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 5024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4771 1.87 - 3.74: 1779 3.74 - 5.61: 278 5.61 - 7.49: 34 7.49 - 9.36: 1 Bond angle restraints: 6863 Sorted by residual: angle pdb=" CA ASP H 106 " pdb=" CB ASP H 106 " pdb=" CG ASP H 106 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " pdb=" CG1 VAL L 163 " ideal model delta sigma weight residual 110.40 119.76 -9.36 1.70e+00 3.46e-01 3.03e+01 angle pdb=" N LYS H 143 " pdb=" CA LYS H 143 " pdb=" C LYS H 143 " ideal model delta sigma weight residual 111.69 118.38 -6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" CA PHE H 78 " pdb=" CB PHE H 78 " pdb=" CG PHE H 78 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CB HIS H 53 " pdb=" CG HIS H 53 " pdb=" CD2 HIS H 53 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 6858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2762 17.30 - 34.60: 204 34.60 - 51.90: 28 51.90 - 69.21: 11 69.21 - 86.51: 4 Dihedral angle restraints: 3009 sinusoidal: 1171 harmonic: 1838 Sorted by residual: dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO H 185 " pdb=" C PRO H 185 " pdb=" N SER H 186 " pdb=" CA SER H 186 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA VAL L 109 " pdb=" C VAL L 109 " pdb=" N LEU L 110 " pdb=" CA LEU L 110 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 3006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 534 0.104 - 0.207: 191 0.207 - 0.311: 29 0.311 - 0.414: 8 0.414 - 0.518: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA SER H 15 " pdb=" N SER H 15 " pdb=" C SER H 15 " pdb=" CB SER H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 761 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 152 " 0.143 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP L 152 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP L 152 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 152 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP L 152 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP L 152 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP L 152 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 152 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 152 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP L 152 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " 0.131 2.00e-02 2.50e+03 7.23e-02 1.05e+02 pdb=" CG TYR A 495 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " -0.114 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR L 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " -0.096 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2340 2.99 - 3.47: 4488 3.47 - 3.94: 8045 3.94 - 4.42: 8899 4.42 - 4.90: 15303 Nonbonded interactions: 39075 Sorted by model distance: nonbonded pdb=" N GLU L 51 " pdb=" O GLU L 51 " model vdw 2.512 2.496 nonbonded pdb=" OD2 ASP L 68 " pdb=" OG SER L 71 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP L 68 " pdb=" OG SER L 70 " model vdw 2.562 3.040 nonbonded pdb=" OH TYR H 145 " pdb=" OE2 GLU H 148 " model vdw 2.568 3.040 nonbonded pdb=" OE2 GLU L 128 " pdb=" OG1 THR L 135 " model vdw 2.568 3.040 ... (remaining 39070 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: 0.010 Normalize map: mean=0, sd=1: 3.440 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.012 0.065 5029 Z= 0.809 Angle : 1.874 9.357 6863 Z= 1.252 Chirality : 0.108 0.518 764 Planarity : 0.015 0.172 881 Dihedral : 13.017 86.508 1813 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 7.32 % 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: -0.73 (0.32), residues: 629 helix: -3.61 (0.50), residues: 41 sheet: 0.44 (0.37), residues: 200 loop : -0.61 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.143 0.019 TRP L 152 HIS 0.011 0.004 HIS H 164 PHE 0.074 0.014 PHE H 29 TYR 0.131 0.021 TYR A 495 ARG 0.008 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7689 (p0) cc_final: 0.7397 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.4038 time to fit residues: 55.6933 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 437 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.054593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039460 restraints weight = 21581.175| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.44 r_work: 0.2754 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5029 Z= 0.177 Angle : 0.626 5.430 6863 Z= 0.346 Chirality : 0.047 0.185 764 Planarity : 0.005 0.042 881 Dihedral : 6.182 24.449 727 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.55 % Allowed : 5.69 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.25 (0.32), residues: 629 helix: -2.68 (0.71), residues: 41 sheet: 0.51 (0.34), residues: 218 loop : -0.22 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 152 HIS 0.002 0.001 HIS H 53 PHE 0.019 0.001 PHE H 78 TYR 0.025 0.001 TYR A 369 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9385 (p0) cc_final: 0.9118 (p0) REVERT: L 84 GLU cc_start: 0.9032 (pm20) cc_final: 0.8608 (pm20) REVERT: L 85 ASP cc_start: 0.8026 (m-30) cc_final: 0.7772 (m-30) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 1.7186 time to fit residues: 50.9681 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN H 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.054481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039314 restraints weight = 21395.986| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.37 r_work: 0.2757 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5029 Z= 0.185 Angle : 0.559 5.656 6863 Z= 0.306 Chirality : 0.046 0.182 764 Planarity : 0.005 0.046 881 Dihedral : 5.365 21.831 727 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.37 % Allowed : 6.97 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.07 (0.33), residues: 629 helix: -2.88 (0.62), residues: 41 sheet: 0.63 (0.35), residues: 226 loop : -0.06 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 189 HIS 0.002 0.001 HIS L 192 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR A 369 ARG 0.009 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9354 (p0) cc_final: 0.9071 (p0) REVERT: A 516 GLU cc_start: 0.8742 (pt0) cc_final: 0.8265 (pm20) REVERT: L 85 ASP cc_start: 0.8039 (m-30) cc_final: 0.7534 (m-30) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 1.2190 time to fit residues: 36.3705 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 30 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.055103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039907 restraints weight = 21632.668| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.43 r_work: 0.2778 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5029 Z= 0.140 Angle : 0.528 8.545 6863 Z= 0.283 Chirality : 0.045 0.173 764 Planarity : 0.005 0.040 881 Dihedral : 4.826 21.276 727 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.92 % Allowed : 8.62 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.04 (0.34), residues: 629 helix: -2.83 (0.73), residues: 34 sheet: 0.69 (0.35), residues: 226 loop : -0.03 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.003 0.001 HIS L 201 PHE 0.011 0.001 PHE H 78 TYR 0.022 0.001 TYR A 369 ARG 0.002 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: A 428 ASP cc_start: 0.9380 (p0) cc_final: 0.9112 (p0) REVERT: A 516 GLU cc_start: 0.8711 (pt0) cc_final: 0.8242 (pm20) REVERT: L 85 ASP cc_start: 0.7984 (m-30) cc_final: 0.7719 (m-30) REVERT: L 164 GLU cc_start: 0.7110 (pm20) cc_final: 0.6853 (pt0) outliers start: 5 outliers final: 0 residues processed: 28 average time/residue: 1.1407 time to fit residues: 33.8738 Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039431 restraints weight = 21903.939| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.31 r_work: 0.2763 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5029 Z= 0.164 Angle : 0.507 7.072 6863 Z= 0.273 Chirality : 0.044 0.168 764 Planarity : 0.005 0.038 881 Dihedral : 4.691 20.539 727 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.55 % Allowed : 11.38 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.06 (0.33), residues: 629 helix: -2.71 (0.74), residues: 34 sheet: 0.76 (0.35), residues: 228 loop : -0.08 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 100 HIS 0.003 0.001 HIS L 201 PHE 0.011 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.002 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8602 (mp0) REVERT: A 428 ASP cc_start: 0.9346 (p0) cc_final: 0.9051 (p0) REVERT: L 86 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8200 (mt-10) outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 1.8657 time to fit residues: 51.1482 Evaluate side-chains 19 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.052114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037330 restraints weight = 21866.942| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.26 r_work: 0.2692 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5029 Z= 0.417 Angle : 0.623 9.903 6863 Z= 0.333 Chirality : 0.047 0.178 764 Planarity : 0.005 0.038 881 Dihedral : 5.403 23.261 727 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.55 % Allowed : 12.66 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.07 (0.33), residues: 629 helix: -2.48 (0.66), residues: 41 sheet: 0.77 (0.35), residues: 226 loop : -0.22 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 154 HIS 0.003 0.001 HIS L 192 PHE 0.012 0.001 PHE H 78 TYR 0.020 0.002 TYR A 369 ARG 0.004 0.001 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8618 (mp0) REVERT: A 428 ASP cc_start: 0.9336 (p0) cc_final: 0.9038 (p0) REVERT: L 85 ASP cc_start: 0.8149 (m-30) cc_final: 0.7710 (m-30) REVERT: L 86 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8173 (mt-10) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 2.3183 time to fit residues: 54.9931 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.053349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038484 restraints weight = 21596.010| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.27 r_work: 0.2730 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5029 Z= 0.201 Angle : 0.551 10.987 6863 Z= 0.292 Chirality : 0.045 0.168 764 Planarity : 0.005 0.038 881 Dihedral : 4.885 21.960 727 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.73 % Allowed : 13.58 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.07 (0.34), residues: 629 helix: -2.21 (0.68), residues: 41 sheet: 0.80 (0.36), residues: 224 loop : -0.09 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100 HIS 0.001 0.000 HIS L 192 PHE 0.011 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8607 (mp0) REVERT: A 428 ASP cc_start: 0.9346 (p0) cc_final: 0.9028 (p0) REVERT: L 85 ASP cc_start: 0.8087 (m-30) cc_final: 0.7877 (m-30) REVERT: L 86 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8041 (mt-10) REVERT: L 164 GLU cc_start: 0.7222 (pm20) cc_final: 0.6431 (pt0) outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 1.1538 time to fit residues: 30.8004 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.053650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038724 restraints weight = 21831.227| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.30 r_work: 0.2738 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5029 Z= 0.172 Angle : 0.540 12.784 6863 Z= 0.282 Chirality : 0.044 0.165 764 Planarity : 0.004 0.038 881 Dihedral : 4.589 21.168 727 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 14.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.20 (0.34), residues: 629 helix: -2.04 (0.81), residues: 34 sheet: 0.90 (0.36), residues: 224 loop : -0.08 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.001 0.000 HIS L 201 PHE 0.010 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.002 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8647 (mp0) REVERT: A 428 ASP cc_start: 0.9346 (p0) cc_final: 0.9035 (p0) REVERT: L 86 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8068 (mt-10) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 1.6066 time to fit residues: 37.7073 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 45 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 = 0.3284 r_free = 0.3284 target = 0.052692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.037811 restraints weight = 21664.229| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.30 r_work: 0.2705 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5029 Z= 0.306 Angle : 0.555 5.001 6863 Z= 0.300 Chirality : 0.045 0.171 764 Planarity : 0.005 0.038 881 Dihedral : 4.931 21.891 727 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.73 % Allowed : 14.13 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.13 (0.34), residues: 629 helix: -2.07 (0.71), residues: 41 sheet: 0.90 (0.36), residues: 222 loop : -0.11 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 154 HIS 0.002 0.001 HIS L 192 PHE 0.012 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.003 0.001 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8634 (mp0) REVERT: A 428 ASP cc_start: 0.9357 (p0) cc_final: 0.9022 (p0) REVERT: L 85 ASP cc_start: 0.8108 (m-30) cc_final: 0.7832 (m-30) REVERT: L 86 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8113 (mt-10) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 1.3545 time to fit residues: 38.7889 Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.053641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038776 restraints weight = 21687.680| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.27 r_work: 0.2741 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5029 Z= 0.172 Angle : 0.562 12.129 6863 Z= 0.294 Chirality : 0.044 0.164 764 Planarity : 0.004 0.037 881 Dihedral : 4.582 21.208 727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.92 % Allowed : 13.94 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.22 (0.34), residues: 629 helix: -2.04 (0.81), residues: 34 sheet: 0.92 (0.36), residues: 224 loop : -0.07 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100 HIS 0.001 0.000 HIS L 192 PHE 0.010 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.002 0.000 ARG H 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.685 Fit side-chains REVERT: A 340 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8657 (mp0) REVERT: A 428 ASP cc_start: 0.9355 (p0) cc_final: 0.9044 (p0) REVERT: L 86 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8013 (mt-10) REVERT: L 114 LYS cc_start: 0.8838 (mttm) cc_final: 0.8424 (tptt) REVERT: L 153 LYS cc_start: 0.9176 (ttpp) cc_final: 0.8469 (tppt) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 1.6871 time to fit residues: 58.5141 Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038806 restraints weight = 21609.631| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.29 r_work: 0.2744 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5029 Z= 0.166 Angle : 0.544 8.076 6863 Z= 0.285 Chirality : 0.044 0.165 764 Planarity : 0.004 0.038 881 Dihedral : 4.463 20.791 727 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.55 % Allowed : 15.05 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.22 (0.34), residues: 629 helix: -2.11 (0.82), residues: 34 sheet: 0.95 (0.36), residues: 224 loop : -0.08 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 189 HIS 0.002 0.000 HIS L 201 PHE 0.010 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.001 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.78 seconds wall clock time: 74 minutes 30.79 seconds (4470.79 seconds total)