Starting phenix.real_space_refine on Sun Mar 10 20:46:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_23709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_23709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_23709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_23709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7b_23709/03_2024/7m7b_23709.pdb" } 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 Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.11, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.75 Conformation dependent library (CDL) restraints added in 896.8 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: 0.66 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: 1.43 Time building geometry restraints manager: 1.86 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: 101.12 - 107.90: 405 107.90 - 114.68: 2514 114.68 - 121.46: 2585 121.46 - 128.24: 1314 128.24 - 135.02: 45 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 2.440 nonbonded pdb=" OD1 ASP L 68 " pdb=" OG SER L 70 " model vdw 2.562 2.440 nonbonded pdb=" OH TYR H 145 " pdb=" OE2 GLU H 148 " model vdw 2.568 2.440 nonbonded pdb=" OE2 GLU L 128 " pdb=" OG1 THR L 135 " model vdw 2.568 2.440 ... (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 ========== 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: 2.070 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: 0.000 Extract box with map and model: 9.670 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.560 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: 1.3931 time to fit residues: 55.4671 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 437 ASN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5029 Z= 0.197 Angle : 0.610 4.835 6863 Z= 0.335 Chirality : 0.047 0.186 764 Planarity : 0.005 0.041 881 Dihedral : 6.169 23.768 727 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.73 % Allowed : 6.06 % Favored : 93.21 % 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: -0.21 (0.32), residues: 629 helix: -2.53 (0.75), residues: 40 sheet: 0.54 (0.34), residues: 218 loop : -0.22 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 152 HIS 0.001 0.001 HIS L 192 PHE 0.019 0.001 PHE H 78 TYR 0.026 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 30 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8158 (p0) cc_final: 0.7739 (p0) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 1.4944 time to fit residues: 43.8468 Evaluate side-chains 18 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 31 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 5029 Z= 0.678 Angle : 0.758 5.565 6863 Z= 0.411 Chirality : 0.052 0.209 764 Planarity : 0.006 0.049 881 Dihedral : 6.661 24.252 727 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.10 % Allowed : 8.44 % 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: -0.57 (0.32), residues: 629 helix: -2.47 (0.74), residues: 34 sheet: 0.48 (0.35), residues: 226 loop : -0.71 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.005 0.002 HIS L 192 PHE 0.014 0.002 PHE A 456 TYR 0.024 0.002 TYR A 369 ARG 0.010 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 26 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8277 (p0) cc_final: 0.7869 (p0) outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 1.0796 time to fit residues: 28.8730 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU 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 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5029 Z= 0.180 Angle : 0.543 6.118 6863 Z= 0.294 Chirality : 0.045 0.173 764 Planarity : 0.005 0.046 881 Dihedral : 5.454 24.051 727 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.10 % Allowed : 9.54 % Favored : 89.36 % 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: -0.23 (0.33), residues: 629 helix: -2.53 (0.70), residues: 40 sheet: 0.73 (0.35), residues: 219 loop : -0.38 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100 HIS 0.002 0.000 HIS L 201 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 *********************** 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 fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8139 (p0) cc_final: 0.7774 (p0) REVERT: L 52 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6583 (m-30) outliers start: 6 outliers final: 1 residues processed: 29 average time/residue: 1.0674 time to fit residues: 33.0130 Evaluate side-chains 22 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5029 Z= 0.240 Angle : 0.564 8.996 6863 Z= 0.301 Chirality : 0.045 0.169 764 Planarity : 0.005 0.050 881 Dihedral : 5.294 23.248 727 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.92 % Allowed : 10.46 % Favored : 88.62 % 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: -0.18 (0.33), residues: 629 helix: -2.54 (0.67), residues: 40 sheet: 0.69 (0.35), residues: 226 loop : -0.30 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.002 0.001 HIS L 192 PHE 0.013 0.001 PHE H 78 TYR 0.021 0.001 TYR A 369 ARG 0.014 0.001 ARG A 346 *********************** 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 23 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8146 (p0) cc_final: 0.7783 (p0) REVERT: L 52 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6598 (m-30) outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 1.1816 time to fit residues: 27.7613 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.004 0.025 5029 Z= 0.242 Angle : 0.534 5.421 6863 Z= 0.289 Chirality : 0.045 0.168 764 Planarity : 0.005 0.043 881 Dihedral : 5.173 23.597 727 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.92 % Allowed : 11.56 % Favored : 87.52 % 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: -0.18 (0.33), residues: 629 helix: -2.49 (0.67), residues: 40 sheet: 0.69 (0.35), residues: 227 loop : -0.31 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100 HIS 0.002 0.000 HIS L 192 PHE 0.013 0.001 PHE H 78 TYR 0.020 0.001 TYR A 369 ARG 0.002 0.000 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 24 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8143 (p0) cc_final: 0.7787 (p0) REVERT: L 164 GLU cc_start: 0.6349 (pm20) cc_final: 0.5685 (pt0) outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 1.0599 time to fit residues: 26.1167 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS 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 43 optimal weight: 0.0020 chunk 33 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5029 Z= 0.148 Angle : 0.527 10.865 6863 Z= 0.277 Chirality : 0.044 0.160 764 Planarity : 0.004 0.042 881 Dihedral : 4.644 23.587 727 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.55 % Allowed : 13.58 % Favored : 85.87 % 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: -0.02 (0.33), residues: 629 helix: -2.77 (0.69), residues: 34 sheet: 0.82 (0.36), residues: 223 loop : -0.22 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 A 457 *********************** 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 23 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8150 (p0) cc_final: 0.7774 (p0) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 1.1990 time to fit residues: 29.3944 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS 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 11 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.0020 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5029 Z= 0.142 Angle : 0.530 8.617 6863 Z= 0.275 Chirality : 0.043 0.156 764 Planarity : 0.004 0.040 881 Dihedral : 4.348 22.439 727 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.10 % Allowed : 13.39 % Favored : 85.50 % 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: 0.10 (0.34), residues: 629 helix: -2.65 (0.69), residues: 34 sheet: 0.90 (0.36), residues: 223 loop : -0.13 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A 457 *********************** 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 33 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.617 Fit side-chains REVERT: A 428 ASP cc_start: 0.8134 (p0) cc_final: 0.7755 (p0) REVERT: H 192 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5831 (pm20) REVERT: L 164 GLU cc_start: 0.5998 (pm20) cc_final: 0.5222 (pt0) outliers start: 6 outliers final: 2 residues processed: 33 average time/residue: 1.4047 time to fit residues: 48.6463 Evaluate side-chains 22 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 192 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3504 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= 0.206 Angle : 0.542 12.163 6863 Z= 0.280 Chirality : 0.044 0.160 764 Planarity : 0.004 0.039 881 Dihedral : 4.527 22.870 727 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.73 % Allowed : 14.50 % Favored : 84.77 % 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: -2.17 (0.73), residues: 40 sheet: 1.01 (0.36), residues: 223 loop : -0.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 189 HIS 0.001 0.000 HIS L 201 PHE 0.012 0.001 PHE H 78 TYR 0.014 0.001 TYR A 369 ARG 0.001 0.000 ARG A 357 *********************** 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 23 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.590 Fit side-chains REVERT: A 428 ASP cc_start: 0.8121 (p0) cc_final: 0.7725 (p0) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 1.2994 time to fit residues: 31.7523 Evaluate side-chains 22 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3514 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= 0.205 Angle : 0.554 12.238 6863 Z= 0.285 Chirality : 0.044 0.160 764 Planarity : 0.004 0.039 881 Dihedral : 4.582 24.030 727 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.55 % Allowed : 14.68 % Favored : 84.77 % 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: 0.11 (0.34), residues: 629 helix: -2.06 (0.75), residues: 40 sheet: 0.85 (0.35), residues: 230 loop : -0.13 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 189 HIS 0.001 0.000 HIS L 192 PHE 0.011 0.001 PHE H 78 TYR 0.014 0.001 TYR A 369 ARG 0.001 0.000 ARG A 403 ********************** 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 22 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.870 Fit side-chains REVERT: A 428 ASP cc_start: 0.8176 (p0) cc_final: 0.7786 (p0) REVERT: L 164 GLU cc_start: 0.6348 (pm20) cc_final: 0.5439 (pt0) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.3615 time to fit residues: 31.7789 Evaluate side-chains 21 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.039085 restraints weight = 21431.213| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.23 r_work: 0.2754 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5029 Z= 0.177 Angle : 0.537 12.278 6863 Z= 0.276 Chirality : 0.043 0.159 764 Planarity : 0.004 0.041 881 Dihedral : 4.458 24.012 727 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.92 % Allowed : 14.13 % Favored : 84.95 % 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: 0.24 (0.34), residues: 629 helix: -2.06 (0.74), residues: 40 sheet: 0.98 (0.36), residues: 222 loop : -0.03 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 189 HIS 0.001 0.000 HIS L 201 PHE 0.011 0.001 PHE H 78 TYR 0.012 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: 1726.99 seconds wall clock time: 31 minutes 58.63 seconds (1918.63 seconds total)