Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 04:08:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/04_2023/6w4s_21539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/04_2023/6w4s_21539.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/6w4s_21539/04_2023/6w4s_21539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/04_2023/6w4s_21539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/04_2023/6w4s_21539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/04_2023/6w4s_21539.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.041 sd= 0.719 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3240 2.51 5 N 814 2.21 5 O 903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 296": "NH1" <-> "NH2" Residue "F ASP 297": "OD1" <-> "OD2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 540": "NH1" <-> "NH2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4986 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3216 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 412} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.00, per 1000 atoms: 0.60 Number of scatterers: 4986 At special positions: 0 Unit cell: (100.158, 98.4608, 92.5192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 903 8.00 N 814 7.00 C 3240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " 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: 2.00 Conformation dependent library (CDL) restraints added in 727.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 60.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 25 through 55 Processing helix chain 'F' and resid 57 through 86 removed outlier: 5.183A pdb=" N ALA F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F 86 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 116 removed outlier: 3.649A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 125 through 157 removed outlier: 4.326A pdb=" N LEU F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.507A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 198 removed outlier: 4.236A pdb=" N LEU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 186 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 200 through 230 removed outlier: 3.694A pdb=" N GLY F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 209 " --> pdb=" O CYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 234 removed outlier: 3.622A pdb=" N ALA F 234 " --> pdb=" O PRO F 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 234' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.694A pdb=" N ASN F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.560A pdb=" N LEU F 317 " --> pdb=" O GLY F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 338 through 367 Processing helix chain 'F' and resid 370 through 393 removed outlier: 3.903A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL F 391 " --> pdb=" O CYS F 387 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 484 removed outlier: 4.547A pdb=" N ILE F 467 " --> pdb=" O ILE F 463 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 514 Processing helix chain 'F' and resid 516 through 546 removed outlier: 4.133A pdb=" N LEU F 525 " --> pdb=" O GLY F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.863A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.628A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.389A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.772A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.736A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1068 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: 1.51 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1053 1.46 - 1.58: 2463 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5101 Sorted by residual: bond pdb=" CA ASP L 86 " pdb=" C ASP L 86 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.80e-02 3.09e+03 1.86e+00 bond pdb=" CG1 ILE H 37 " pdb=" CD1 ILE H 37 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.70e-01 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.468 1.460 0.009 1.05e-02 9.07e+03 6.89e-01 bond pdb=" CB ASP F 473 " pdb=" CG ASP F 473 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.26e-01 bond pdb=" CB ASN L 95 " pdb=" CG ASN L 95 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 ... (remaining 5096 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 125 106.77 - 113.58: 2912 113.58 - 120.39: 1887 120.39 - 127.20: 1976 127.20 - 134.02: 52 Bond angle restraints: 6952 Sorted by residual: angle pdb=" N ILE F 186 " pdb=" CA ILE F 186 " pdb=" C ILE F 186 " ideal model delta sigma weight residual 113.42 110.12 3.30 1.17e+00 7.31e-01 7.93e+00 angle pdb=" C GLY F 55 " pdb=" N ASN F 56 " pdb=" CA ASN F 56 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" C PHE F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta sigma weight residual 120.31 116.82 3.49 1.52e+00 4.33e-01 5.28e+00 angle pdb=" N PRO L 50 " pdb=" CA PRO L 50 " pdb=" C PRO L 50 " ideal model delta sigma weight residual 110.21 113.76 -3.55 1.64e+00 3.72e-01 4.68e+00 angle pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 ... (remaining 6947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2640 16.75 - 33.50: 250 33.50 - 50.25: 46 50.25 - 66.99: 16 66.99 - 83.74: 5 Dihedral angle restraints: 2957 sinusoidal: 1085 harmonic: 1872 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 136.54 -43.54 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LEU L 54 " pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 475 0.027 - 0.053: 211 0.053 - 0.080: 89 0.080 - 0.107: 37 0.107 - 0.133: 12 Chirality restraints: 824 Sorted by residual: chirality pdb=" CA ILE L 52 " pdb=" N ILE L 52 " pdb=" C ILE L 52 " pdb=" CB ILE L 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ASN F 56 " pdb=" N ASN F 56 " pdb=" C ASN F 56 " pdb=" CB ASN F 56 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 821 not shown) Planarity restraints: 849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 516 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO F 517 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 517 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 517 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO L 48 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 846 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5211 3.27 - 3.81: 7917 3.81 - 4.36: 9283 4.36 - 4.90: 16708 Nonbonded interactions: 39386 Sorted by model distance: nonbonded pdb=" OG1 THR F 122 " pdb=" O ARG L 96 " model vdw 2.176 2.440 nonbonded pdb=" NE2 GLN L 93 " pdb=" OD1 ASN L 95 " model vdw 2.210 2.520 nonbonded pdb=" OD1 ASN H 60 " pdb=" OG SER H 62 " model vdw 2.240 2.440 nonbonded pdb=" O VAL F 67 " pdb=" OG SER F 71 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU F 119 " pdb=" OH TYR H 33 " model vdw 2.260 2.440 ... (remaining 39381 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: 1.110 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: 6.190 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.280 Find NCS groups from input model: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.004 0.034 5101 Z= 0.276 Angle : 0.571 5.823 6952 Z= 0.331 Chirality : 0.039 0.133 824 Planarity : 0.004 0.049 849 Dihedral : 14.378 83.741 1757 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.13 (0.33), residues: 640 helix: 0.50 (0.27), residues: 371 sheet: -0.84 (0.53), residues: 100 loop : -3.49 (0.37), residues: 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.580 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1768 time to fit residues: 28.5516 Evaluate side-chains 106 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0593 time to fit residues: 2.7232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN F 99 GLN F 141 ASN F 174 ASN F 304 ASN F 481 GLN F 496 GLN F 516 ASN H 16 GLN H 76 ASN H 77 HIS L 38 HIS L 78 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5101 Z= 0.218 Angle : 0.543 6.503 6952 Z= 0.298 Chirality : 0.040 0.200 824 Planarity : 0.005 0.041 849 Dihedral : 4.271 17.030 698 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.35), residues: 640 helix: 1.76 (0.29), residues: 370 sheet: -0.34 (0.54), residues: 106 loop : -2.85 (0.40), residues: 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.568 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 109 average time/residue: 0.1665 time to fit residues: 23.4375 Evaluate side-chains 95 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0503 time to fit residues: 1.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5101 Z= 0.167 Angle : 0.509 5.973 6952 Z= 0.273 Chirality : 0.039 0.136 824 Planarity : 0.004 0.042 849 Dihedral : 4.036 16.974 698 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.13 (0.35), residues: 640 helix: 2.34 (0.28), residues: 369 sheet: -0.28 (0.54), residues: 104 loop : -2.35 (0.41), residues: 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.720 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.1837 time to fit residues: 29.9049 Evaluate side-chains 102 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0627 time to fit residues: 2.0743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 5101 Z= 0.316 Angle : 0.591 7.302 6952 Z= 0.316 Chirality : 0.042 0.176 824 Planarity : 0.004 0.041 849 Dihedral : 4.335 15.899 698 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.02 (0.35), residues: 640 helix: 2.14 (0.28), residues: 368 sheet: 0.05 (0.54), residues: 102 loop : -2.33 (0.41), residues: 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.583 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1590 time to fit residues: 21.3654 Evaluate side-chains 97 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0510 time to fit residues: 1.7890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5101 Z= 0.185 Angle : 0.526 6.435 6952 Z= 0.282 Chirality : 0.039 0.140 824 Planarity : 0.004 0.043 849 Dihedral : 4.092 16.443 698 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.42 (0.35), residues: 640 helix: 2.37 (0.28), residues: 375 sheet: -0.02 (0.55), residues: 100 loop : -1.91 (0.44), residues: 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.526 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.1556 time to fit residues: 20.2748 Evaluate side-chains 94 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0573 time to fit residues: 1.0986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 5101 Z= 0.166 Angle : 0.517 7.269 6952 Z= 0.275 Chirality : 0.039 0.174 824 Planarity : 0.004 0.042 849 Dihedral : 3.993 17.227 698 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.60 (0.35), residues: 640 helix: 2.49 (0.28), residues: 375 sheet: 0.03 (0.55), residues: 99 loop : -1.75 (0.45), residues: 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.650 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 0.1508 time to fit residues: 20.4599 Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0487 time to fit residues: 0.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5101 Z= 0.214 Angle : 0.551 6.960 6952 Z= 0.291 Chirality : 0.040 0.161 824 Planarity : 0.004 0.042 849 Dihedral : 4.063 16.466 698 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.57 (0.35), residues: 640 helix: 2.37 (0.27), residues: 375 sheet: 0.06 (0.53), residues: 106 loop : -1.57 (0.48), residues: 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.583 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1563 time to fit residues: 19.8744 Evaluate side-chains 96 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0524 time to fit residues: 1.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 5101 Z= 0.327 Angle : 0.642 16.603 6952 Z= 0.330 Chirality : 0.042 0.190 824 Planarity : 0.004 0.040 849 Dihedral : 4.378 16.925 698 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.27 (0.35), residues: 640 helix: 2.12 (0.27), residues: 374 sheet: 0.12 (0.54), residues: 102 loop : -1.75 (0.46), residues: 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.610 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.1524 time to fit residues: 19.2076 Evaluate side-chains 88 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0465 time to fit residues: 1.0845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 5101 Z= 0.160 Angle : 0.531 6.218 6952 Z= 0.280 Chirality : 0.039 0.182 824 Planarity : 0.004 0.043 849 Dihedral : 3.996 17.507 698 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.73 (0.35), residues: 640 helix: 2.46 (0.27), residues: 375 sheet: 0.27 (0.55), residues: 101 loop : -1.49 (0.48), residues: 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.512 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.1624 time to fit residues: 21.9591 Evaluate side-chains 95 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0517 time to fit residues: 0.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5101 Z= 0.185 Angle : 0.564 7.646 6952 Z= 0.293 Chirality : 0.041 0.274 824 Planarity : 0.004 0.043 849 Dihedral : 4.036 16.762 698 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.68 (0.35), residues: 640 helix: 2.43 (0.27), residues: 375 sheet: -0.03 (0.52), residues: 104 loop : -1.33 (0.49), residues: 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.624 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1548 time to fit residues: 20.0703 Evaluate side-chains 93 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113809 restraints weight = 7554.718| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.73 r_work: 0.3364 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 5101 Z= 0.163 Angle : 0.553 7.048 6952 Z= 0.288 Chirality : 0.040 0.164 824 Planarity : 0.004 0.043 849 Dihedral : 3.934 16.818 698 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.79 (0.35), residues: 640 helix: 2.49 (0.27), residues: 375 sheet: 0.01 (0.52), residues: 104 loop : -1.21 (0.50), residues: 161 =============================================================================== Job complete usr+sys time: 1375.05 seconds wall clock time: 25 minutes 38.80 seconds (1538.80 seconds total)