Starting phenix.real_space_refine on Sun Mar 10 18:18:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/03_2024/8j97_36090_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 13 5.16 5 C 2466 2.51 5 N 649 2.21 5 O 731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3863 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2196 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 289} Chain breaks: 6 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 182 Chain: "H" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 864 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 729 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.65, per 1000 atoms: 0.69 Number of scatterers: 3863 At special positions: 0 Unit cell: (55.2967, 103.85, 83.6194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 4 15.00 O 731 8.00 N 649 7.00 C 2466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 12 sheets defined 4.6% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.530A pdb=" N PHE A 117 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.384A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 57 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS A 59 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL A 81 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.557A pdb=" N ARG A 188 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 344 through 349 removed outlier: 4.076A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.512A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.578A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.820A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'L' and resid 20 through 25 Processing sheet with id= L, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.625A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 345 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: 1.14 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 627 1.32 - 1.44: 1050 1.44 - 1.56: 2239 1.56 - 1.69: 11 1.69 - 1.81: 17 Bond restraints: 3944 Sorted by residual: bond pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 1.717 1.599 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" OG1 TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O1P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O2P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.09: 128 106.09 - 113.06: 2153 113.06 - 120.02: 1221 120.02 - 126.99: 1869 126.99 - 133.95: 43 Bond angle restraints: 5414 Sorted by residual: angle pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta sigma weight residual 121.97 129.37 -7.40 1.00e+00 1.00e+00 5.48e+01 angle pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " pdb=" CG PHE A 115 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.35e+01 angle pdb=" C PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 111.56 101.98 9.58 1.65e+00 3.67e-01 3.37e+01 angle pdb=" N VAL A 343 " pdb=" CA VAL A 343 " pdb=" CB VAL A 343 " ideal model delta sigma weight residual 109.84 116.68 -6.84 1.32e+00 5.74e-01 2.68e+01 angle pdb=" CB TPO V 307 " pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 119.31 104.93 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2140 17.85 - 35.70: 136 35.70 - 53.55: 29 53.55 - 71.40: 1 71.40 - 89.25: 5 Dihedral angle restraints: 2311 sinusoidal: 732 harmonic: 1579 Sorted by residual: dihedral pdb=" CA LYS A 229 " pdb=" C LYS A 229 " pdb=" N LYS A 230 " pdb=" CA LYS A 230 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ASP A 342 " pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN L 90 " pdb=" C GLN L 90 " pdb=" N GLN L 91 " pdb=" CA GLN L 91 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 456 0.046 - 0.091: 140 0.091 - 0.137: 48 0.137 - 0.183: 5 0.183 - 0.228: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB VAL A 343 " pdb=" CA VAL A 343 " pdb=" CG1 VAL A 343 " pdb=" CG2 VAL A 343 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 647 not shown) Planarity restraints: 692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " -0.024 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE A 115 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 353 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 354 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 182 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " 0.022 5.00e-02 4.00e+02 ... (remaining 689 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 950 2.79 - 3.32: 3402 3.32 - 3.85: 6118 3.85 - 4.37: 7007 4.37 - 4.90: 12445 Nonbonded interactions: 29922 Sorted by model distance: nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.266 2.440 nonbonded pdb=" NH2 ARG A 7 " pdb=" OG SEP V 309 " model vdw 2.314 2.520 nonbonded pdb=" O THR A 221 " pdb=" OG1 THR A 221 " model vdw 2.326 2.440 nonbonded pdb=" NH2 ARG A 25 " pdb=" O VAL A 167 " model vdw 2.331 2.520 nonbonded pdb=" OD1 ASN H 31 " pdb=" N VAL H 32 " model vdw 2.347 2.520 ... (remaining 29917 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: 0.800 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: 3.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.007 0.118 3944 Z= 0.453 Angle : 0.915 14.385 5414 Z= 0.483 Chirality : 0.050 0.228 650 Planarity : 0.006 0.053 692 Dihedral : 13.201 89.250 1285 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.28 % Allowed : 10.42 % Favored : 89.30 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -1.02 (0.37), residues: 517 helix: -1.09 (1.28), residues: 18 sheet: -0.98 (0.34), residues: 237 loop : -0.15 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.039 0.003 PHE A 115 TYR 0.022 0.002 TYR A 21 ARG 0.004 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.419 Fit side-chains REVERT: A 169 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7611 (mtm180) REVERT: H 33 TYR cc_start: 0.7978 (m-80) cc_final: 0.7644 (m-80) REVERT: H 86 MET cc_start: 0.7488 (mtt) cc_final: 0.7278 (mtm) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1550 time to fit residues: 17.1565 Evaluate side-chains 88 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.0060 chunk 14 optimal weight: 0.0970 overall best weight: 0.1512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3944 Z= 0.173 Angle : 0.597 10.941 5414 Z= 0.305 Chirality : 0.045 0.168 650 Planarity : 0.005 0.037 692 Dihedral : 5.479 45.790 582 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.25 % Allowed : 10.99 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.55 (0.39), residues: 517 helix: -0.65 (1.09), residues: 24 sheet: -0.62 (0.34), residues: 239 loop : 0.14 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.001 0.000 HIS A 353 PHE 0.011 0.002 PHE A 277 TYR 0.020 0.001 TYR A 21 ARG 0.003 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.423 Fit side-chains REVERT: A 122 ASN cc_start: 0.7906 (t0) cc_final: 0.7311 (m-40) REVERT: A 169 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7309 (mtm180) REVERT: H 9 GLU cc_start: 0.7285 (mp0) cc_final: 0.7005 (mp0) REVERT: H 86 MET cc_start: 0.7407 (mtt) cc_final: 0.7190 (mtm) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.1664 time to fit residues: 18.4541 Evaluate side-chains 90 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3944 Z= 0.301 Angle : 0.637 10.582 5414 Z= 0.326 Chirality : 0.047 0.157 650 Planarity : 0.005 0.049 692 Dihedral : 5.690 45.987 582 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.66 % Allowed : 11.83 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.58 (0.38), residues: 517 helix: -0.84 (1.05), residues: 24 sheet: -0.50 (0.35), residues: 242 loop : -0.02 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 113 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.002 PHE H 105 TYR 0.025 0.002 TYR A 21 ARG 0.005 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.417 Fit side-chains REVERT: A 122 ASN cc_start: 0.8034 (t0) cc_final: 0.7756 (t0) REVERT: A 169 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7485 (mtm180) REVERT: H 9 GLU cc_start: 0.7329 (mp0) cc_final: 0.6949 (mp0) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.1426 time to fit residues: 17.3196 Evaluate side-chains 99 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3944 Z= 0.295 Angle : 0.622 9.801 5414 Z= 0.318 Chirality : 0.047 0.160 650 Planarity : 0.005 0.051 692 Dihedral : 5.564 43.104 581 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.38 % Allowed : 12.96 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.60 (0.39), residues: 517 helix: -0.73 (1.09), residues: 24 sheet: -0.49 (0.34), residues: 254 loop : -0.02 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 113 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.002 PHE H 105 TYR 0.024 0.002 TYR A 21 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.404 Fit side-chains REVERT: A 122 ASN cc_start: 0.8035 (t0) cc_final: 0.7756 (t0) REVERT: H 9 GLU cc_start: 0.7334 (mp0) cc_final: 0.6932 (mp0) REVERT: H 34 SER cc_start: 0.8475 (t) cc_final: 0.8261 (t) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.1412 time to fit residues: 17.0625 Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.0020 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 237 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3944 Z= 0.224 Angle : 0.571 9.425 5414 Z= 0.292 Chirality : 0.045 0.147 650 Planarity : 0.005 0.046 692 Dihedral : 5.288 40.616 581 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.94 % Allowed : 14.37 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.50 (0.39), residues: 517 helix: -0.52 (1.11), residues: 24 sheet: -0.41 (0.34), residues: 252 loop : -0.01 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.013 0.002 PHE A 277 TYR 0.020 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7997 (t0) cc_final: 0.7736 (t0) outliers start: 14 outliers final: 13 residues processed: 92 average time/residue: 0.1353 time to fit residues: 16.1019 Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 48 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3944 Z= 0.237 Angle : 0.572 9.172 5414 Z= 0.292 Chirality : 0.046 0.150 650 Planarity : 0.005 0.047 692 Dihedral : 5.219 39.097 581 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.94 % Allowed : 14.65 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.46 (0.39), residues: 517 helix: -0.47 (1.11), residues: 24 sheet: -0.39 (0.34), residues: 252 loop : 0.01 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.002 PHE A 277 TYR 0.020 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.380 Fit side-chains REVERT: A 122 ASN cc_start: 0.8002 (t0) cc_final: 0.7754 (t0) REVERT: H 9 GLU cc_start: 0.7335 (mp0) cc_final: 0.7055 (mp0) REVERT: L 37 TYR cc_start: 0.7065 (m-80) cc_final: 0.6829 (m-80) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.1313 time to fit residues: 15.4851 Evaluate side-chains 97 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3944 Z= 0.238 Angle : 0.579 9.060 5414 Z= 0.294 Chirality : 0.046 0.164 650 Planarity : 0.005 0.047 692 Dihedral : 5.193 38.661 581 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.66 % Allowed : 15.21 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.46 (0.39), residues: 517 helix: -0.45 (1.10), residues: 24 sheet: -0.38 (0.34), residues: 252 loop : 0.00 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.002 PHE A 277 TYR 0.020 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.583 Fit side-chains REVERT: A 122 ASN cc_start: 0.8021 (t0) cc_final: 0.7785 (t0) REVERT: H 9 GLU cc_start: 0.7323 (mp0) cc_final: 0.7039 (mp0) REVERT: L 37 TYR cc_start: 0.7052 (m-80) cc_final: 0.6819 (m-80) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.1602 time to fit residues: 19.0602 Evaluate side-chains 99 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.184 Angle : 0.551 8.930 5414 Z= 0.280 Chirality : 0.045 0.156 650 Planarity : 0.004 0.042 692 Dihedral : 4.985 37.957 581 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.41 (0.40), residues: 517 helix: -0.37 (1.10), residues: 24 sheet: -0.33 (0.34), residues: 254 loop : 0.02 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.009 0.001 PHE A 277 TYR 0.017 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.450 Fit side-chains REVERT: A 122 ASN cc_start: 0.7945 (t0) cc_final: 0.7702 (t0) REVERT: H 9 GLU cc_start: 0.7315 (mp0) cc_final: 0.7044 (mp0) REVERT: L 37 TYR cc_start: 0.7076 (m-80) cc_final: 0.6834 (m-80) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 0.1333 time to fit residues: 15.9862 Evaluate side-chains 99 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.0020 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 41 optimal weight: 0.0970 chunk 4 optimal weight: 0.0770 overall best weight: 0.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3944 Z= 0.170 Angle : 0.546 8.877 5414 Z= 0.272 Chirality : 0.045 0.146 650 Planarity : 0.004 0.042 692 Dihedral : 4.790 37.271 581 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.25 % Allowed : 18.31 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.28 (0.40), residues: 517 helix: -0.26 (1.11), residues: 24 sheet: -0.26 (0.34), residues: 255 loop : 0.13 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.010 0.001 PHE A 277 TYR 0.015 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.384 Fit side-chains REVERT: A 122 ASN cc_start: 0.7918 (t0) cc_final: 0.7697 (t0) REVERT: H 9 GLU cc_start: 0.7310 (mp0) cc_final: 0.7047 (mp0) REVERT: H 86 MET cc_start: 0.7428 (mtt) cc_final: 0.7154 (mtm) REVERT: L 37 TYR cc_start: 0.7021 (m-80) cc_final: 0.6759 (m-80) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1372 time to fit residues: 16.4443 Evaluate side-chains 97 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 41 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3944 Z= 0.210 Angle : 0.568 9.655 5414 Z= 0.286 Chirality : 0.046 0.163 650 Planarity : 0.004 0.045 692 Dihedral : 4.902 37.725 581 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.97 % Allowed : 19.44 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.30 (0.40), residues: 517 helix: -0.34 (1.10), residues: 24 sheet: -0.26 (0.34), residues: 254 loop : 0.10 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.010 0.002 PHE A 277 TYR 0.018 0.001 TYR A 21 ARG 0.003 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.467 Fit side-chains REVERT: A 122 ASN cc_start: 0.8034 (t0) cc_final: 0.7792 (t0) REVERT: H 9 GLU cc_start: 0.7316 (mp0) cc_final: 0.7014 (mp0) REVERT: L 37 TYR cc_start: 0.7038 (m-80) cc_final: 0.6766 (m-80) outliers start: 7 outliers final: 7 residues processed: 94 average time/residue: 0.1291 time to fit residues: 15.6583 Evaluate side-chains 97 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** 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 = 0.3949 r_free = 0.3949 target = 0.144690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133790 restraints weight = 5610.475| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.93 r_work: 0.3721 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3944 Z= 0.240 Angle : 0.589 9.957 5414 Z= 0.297 Chirality : 0.046 0.165 650 Planarity : 0.005 0.046 692 Dihedral : 5.050 37.906 581 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.25 % Allowed : 19.44 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -0.42 (0.39), residues: 517 helix: -0.38 (1.10), residues: 24 sheet: -0.35 (0.34), residues: 255 loop : 0.03 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.002 PHE H 105 TYR 0.019 0.002 TYR A 21 ARG 0.002 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.66 seconds wall clock time: 26 minutes 13.08 seconds (1573.08 seconds total)