Starting phenix.real_space_refine on Fri Dec 8 00:39:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl8_27499/12_2023/8dl8_27499.pdb" } resolution = 3.0 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= 0.002 sd= 0.062 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 Co 2 6.85 5 S 34 5.16 5 C 3969 2.51 5 N 1049 2.21 5 O 1154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3387 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1373 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1445 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 79} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2052 SG CYS A 326 23.364 42.046 35.119 1.00104.32 S Time building chain proxies: 4.25, per 1000 atoms: 0.68 Number of scatterers: 6208 At special positions: 0 Unit cell: (73.44, 74.52, 145.8, 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) Co 2 26.99 S 34 16.00 O 1154 8.00 N 1049 7.00 C 3969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 49.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.745A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.563A pdb=" N HIS A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 126 through 156 removed outlier: 3.597A pdb=" N ARG A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.740A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 305 removed outlier: 4.667A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.262A pdb=" N GLY A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 368 through 392 removed outlier: 3.748A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 483 Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 547 Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.052A pdb=" N LEU C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.931A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.652A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.730A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.908A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 158 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.537A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 149 removed outlier: 4.103A pdb=" N LEU D 166 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 164 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 176 through 179 439 hydrogen bonds defined for protein. 1251 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: 2.19 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2020 1.34 - 1.46: 1505 1.46 - 1.58: 2742 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 6322 Sorted by residual: bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" N GLU D 61 " pdb=" CA GLU D 61 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.18e+00 bond pdb=" CG PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.11e+00 bond pdb=" C ILE A 463 " pdb=" O ILE A 463 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.60e-01 bond pdb=" CB ILE A 467 " pdb=" CG2 ILE A 467 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 ... (remaining 6317 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 102 106.08 - 113.06: 3477 113.06 - 120.05: 2034 120.05 - 127.03: 2955 127.03 - 134.01: 55 Bond angle restraints: 8623 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 107.19 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" N PRO C 60 " pdb=" CA PRO C 60 " pdb=" C PRO C 60 " ideal model delta sigma weight residual 110.21 113.94 -3.73 1.64e+00 3.72e-01 5.19e+00 angle pdb=" CG ARG A 365 " pdb=" CD ARG A 365 " pdb=" NE ARG A 365 " ideal model delta sigma weight residual 112.00 116.66 -4.66 2.20e+00 2.07e-01 4.48e+00 angle pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" C GLU A 290 " ideal model delta sigma weight residual 109.81 114.48 -4.67 2.21e+00 2.05e-01 4.46e+00 angle pdb=" CA PRO D 33 " pdb=" N PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 112.00 109.24 2.76 1.40e+00 5.10e-01 3.89e+00 ... (remaining 8618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3202 17.96 - 35.91: 336 35.91 - 53.87: 128 53.87 - 71.83: 10 71.83 - 89.78: 3 Dihedral angle restraints: 3679 sinusoidal: 1170 harmonic: 2509 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual -86.00 -113.49 27.49 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA ASN A 141 " pdb=" CB ASN A 141 " pdb=" CG ASN A 141 " pdb=" OD1 ASN A 141 " ideal model delta sinusoidal sigma weight residual 120.00 -169.77 -70.23 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP D 80 " pdb=" CB ASP D 80 " pdb=" CG ASP D 80 " pdb=" OD1 ASP D 80 " ideal model delta sinusoidal sigma weight residual -30.00 -84.96 54.96 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 605 0.027 - 0.054: 263 0.054 - 0.081: 89 0.081 - 0.108: 52 0.108 - 0.135: 17 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CB ILE A 467 " pdb=" CA ILE A 467 " pdb=" CG1 ILE A 467 " pdb=" CG2 ILE A 467 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1023 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO D 33 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.066 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 517 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 59 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 60 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.049 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 2691 2.93 - 3.58: 8950 3.58 - 4.24: 12970 4.24 - 4.90: 22833 Nonbonded interactions: 47449 Sorted by model distance: nonbonded pdb=" SG CYS A 326 " pdb="CO CO A 602 " model vdw 1.612 2.580 nonbonded pdb=" OD2 ASP A 39 " pdb="CO CO A 601 " model vdw 2.026 2.220 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 602 " model vdw 2.130 2.300 nonbonded pdb=" NE2 HIS A 43 " pdb="CO CO A 601 " model vdw 2.145 2.300 nonbonded pdb=" OG SER C 34 " pdb=" OD2 ASP C 37 " model vdw 2.239 2.440 ... (remaining 47444 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: 0.340 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: 2.000 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.003 0.066 6322 Z= 0.176 Angle : 0.534 6.857 8623 Z= 0.285 Chirality : 0.040 0.135 1026 Planarity : 0.007 0.102 1095 Dihedral : 16.820 89.785 2066 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 3.54 % Allowed : 35.40 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.02 (0.30), residues: 867 helix: 2.75 (0.25), residues: 402 sheet: 1.13 (0.41), residues: 198 loop : -0.77 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 69 HIS 0.003 0.001 HIS A 32 PHE 0.009 0.001 PHE C 107 TYR 0.008 0.001 TYR A 64 ARG 0.007 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.642 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 0.9928 time to fit residues: 205.5264 Evaluate side-chains 136 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1361 time to fit residues: 1.1366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 118 HIS A 182 GLN C 48 ASN D 22 GLN D 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6322 Z= 0.337 Angle : 0.621 7.657 8623 Z= 0.325 Chirality : 0.042 0.177 1026 Planarity : 0.005 0.067 1095 Dihedral : 3.618 14.153 926 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 9.03 % Allowed : 31.33 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.34 (0.29), residues: 867 helix: 2.94 (0.25), residues: 409 sheet: 1.17 (0.38), residues: 207 loop : -0.54 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.010 0.002 HIS A 118 PHE 0.014 0.001 PHE C 107 TYR 0.012 0.001 TYR C 160 ARG 0.007 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 117 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 20 residues processed: 155 average time/residue: 0.9945 time to fit residues: 162.8466 Evaluate side-chains 124 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4284 time to fit residues: 2.8703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 50.0000 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN A 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6322 Z= 0.179 Angle : 0.583 7.873 8623 Z= 0.292 Chirality : 0.041 0.182 1026 Planarity : 0.004 0.058 1095 Dihedral : 3.451 13.096 926 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 7.61 % Allowed : 31.68 % Favored : 60.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.52 (0.30), residues: 867 helix: 3.17 (0.25), residues: 408 sheet: 1.20 (0.38), residues: 209 loop : -0.55 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.010 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.011 0.001 TYR C 69 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 151 average time/residue: 1.0133 time to fit residues: 161.4746 Evaluate side-chains 133 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.6336 time to fit residues: 4.3527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 83 optimal weight: 40.0000 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 48 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.035 6322 Z= 0.226 Angle : 0.590 8.541 8623 Z= 0.297 Chirality : 0.041 0.166 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.443 13.523 926 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 6.73 % Allowed : 32.92 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.62 (0.30), residues: 867 helix: 3.21 (0.25), residues: 407 sheet: 1.33 (0.38), residues: 203 loop : -0.45 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.010 0.002 HIS A 118 PHE 0.012 0.001 PHE C 30 TYR 0.011 0.001 TYR C 69 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 147 average time/residue: 0.9912 time to fit residues: 154.0145 Evaluate side-chains 126 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.0587 time to fit residues: 1.1711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6322 Z= 0.377 Angle : 0.657 8.591 8623 Z= 0.340 Chirality : 0.043 0.176 1026 Planarity : 0.004 0.052 1095 Dihedral : 3.579 14.888 926 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 7.43 % Allowed : 32.74 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.42 (0.30), residues: 867 helix: 2.97 (0.25), residues: 409 sheet: 1.24 (0.38), residues: 204 loop : -0.44 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.012 0.002 HIS A 118 PHE 0.009 0.001 PHE C 107 TYR 0.015 0.001 TYR C 160 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 0.737 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 140 average time/residue: 1.0447 time to fit residues: 154.7118 Evaluate side-chains 123 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.0709 time to fit residues: 1.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 40.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6322 Z= 0.278 Angle : 0.641 9.643 8623 Z= 0.324 Chirality : 0.042 0.185 1026 Planarity : 0.004 0.051 1095 Dihedral : 3.534 14.139 926 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 7.26 % Allowed : 34.16 % Favored : 58.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.48 (0.30), residues: 867 helix: 3.13 (0.25), residues: 401 sheet: 1.22 (0.37), residues: 204 loop : -0.46 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.011 0.002 HIS A 118 PHE 0.010 0.001 PHE A 324 TYR 0.010 0.001 TYR C 160 ARG 0.006 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 141 average time/residue: 1.0119 time to fit residues: 150.9658 Evaluate side-chains 133 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.3478 time to fit residues: 3.2853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6322 Z= 0.239 Angle : 0.655 10.256 8623 Z= 0.324 Chirality : 0.042 0.186 1026 Planarity : 0.004 0.051 1095 Dihedral : 3.520 14.304 926 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 6.90 % Allowed : 35.93 % Favored : 57.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.55 (0.30), residues: 867 helix: 3.14 (0.26), residues: 402 sheet: 1.29 (0.38), residues: 202 loop : -0.37 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.012 0.002 HIS A 118 PHE 0.015 0.001 PHE C 30 TYR 0.010 0.001 TYR C 69 ARG 0.011 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 141 average time/residue: 1.0118 time to fit residues: 150.8167 Evaluate side-chains 132 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 1.7849 time to fit residues: 2.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6322 Z= 0.224 Angle : 0.673 11.200 8623 Z= 0.329 Chirality : 0.042 0.215 1026 Planarity : 0.004 0.051 1095 Dihedral : 3.480 13.372 926 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 5.66 % Allowed : 37.70 % Favored : 56.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.54 (0.30), residues: 867 helix: 3.11 (0.25), residues: 402 sheet: 1.30 (0.38), residues: 202 loop : -0.35 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.012 0.002 HIS A 118 PHE 0.007 0.001 PHE A 324 TYR 0.009 0.001 TYR C 69 ARG 0.007 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.720 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 143 average time/residue: 1.0011 time to fit residues: 151.3486 Evaluate side-chains 129 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 0.9815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6322 Z= 0.232 Angle : 0.710 12.288 8623 Z= 0.344 Chirality : 0.043 0.252 1026 Planarity : 0.004 0.050 1095 Dihedral : 3.491 14.313 926 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 5.84 % Allowed : 38.05 % Favored : 56.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.53 (0.30), residues: 867 helix: 3.09 (0.26), residues: 401 sheet: 1.30 (0.38), residues: 202 loop : -0.33 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.005 0.001 HIS A 118 PHE 0.015 0.001 PHE C 30 TYR 0.009 0.001 TYR C 69 ARG 0.007 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 140 average time/residue: 0.9391 time to fit residues: 139.4656 Evaluate side-chains 129 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 1.7759 time to fit residues: 2.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 144 ASN A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6322 Z= 0.265 Angle : 0.743 14.902 8623 Z= 0.357 Chirality : 0.044 0.246 1026 Planarity : 0.004 0.058 1095 Dihedral : 3.583 18.635 926 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 5.13 % Allowed : 39.29 % Favored : 55.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.50 (0.30), residues: 867 helix: 3.04 (0.25), residues: 401 sheet: 1.36 (0.38), residues: 202 loop : -0.36 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.015 0.002 HIS A 118 PHE 0.008 0.001 PHE A 324 TYR 0.010 0.001 TYR C 69 ARG 0.015 0.001 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 133 average time/residue: 1.0195 time to fit residues: 143.3037 Evaluate side-chains 126 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 1 average time/residue: 0.2089 time to fit residues: 1.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 40.0000 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.057206 restraints weight = 18305.919| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.61 r_work: 0.2644 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6322 Z= 0.281 Angle : 0.765 13.867 8623 Z= 0.370 Chirality : 0.044 0.254 1026 Planarity : 0.004 0.049 1095 Dihedral : 3.603 17.880 926 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 4.96 % Allowed : 39.82 % Favored : 55.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.41 (0.29), residues: 867 helix: 2.99 (0.25), residues: 401 sheet: 1.29 (0.38), residues: 202 loop : -0.42 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.007 0.001 HIS A 118 PHE 0.016 0.001 PHE C 30 TYR 0.009 0.001 TYR C 69 ARG 0.007 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.18 seconds wall clock time: 50 minutes 15.23 seconds (3015.23 seconds total)