Starting phenix.real_space_refine (version: dev) on Fri Feb 17 16:19:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/02_2023/7ura_26707_updated.pdb" } resolution = 3.11 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= 0.007 sd= 0.122 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 Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 103": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'OH6': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 54.449 29.304 19.614 1.00100.07 S ATOM 2880 SG CYS A 376 53.464 29.646 22.508 1.00107.56 S ATOM 2908 SG CYS A 380 56.441 28.777 22.619 1.00114.72 S Time building chain proxies: 3.76, per 1000 atoms: 0.70 Number of scatterers: 5400 At special positions: 0 Unit cell: (97.11, 68.89, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 3 15.00 O 945 8.00 N 869 7.00 C 3550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 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: 2.12 Conformation dependent library (CDL) restraints added in 821.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 370 " Number of angles added : 3 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 7 sheets defined 48.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 removed outlier: 4.505A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 44 removed outlier: 5.127A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 71 through 88 removed outlier: 4.218A pdb=" N LEU A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.577A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 187 through 209 Processing helix chain 'A' and resid 236 through 262 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 302 through 319 removed outlier: 5.912A pdb=" N ARG A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 343 through 367 Processing helix chain 'A' and resid 389 through 411 removed outlier: 4.977A pdb=" N LEU A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.604A pdb=" N GLN L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 30 through 33 removed outlier: 5.847A pdb=" N LYS L 123 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA L 33 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU L 125 " --> pdb=" O ALA L 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'L' and resid 105 through 110 removed outlier: 6.434A pdb=" N GLN L 57 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU L 66 " --> pdb=" O GLN L 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= E, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.275A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= G, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.715A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 759 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: 1.70 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 3 1.19 - 1.39: 2276 1.39 - 1.59: 3198 1.59 - 1.79: 45 1.79 - 1.99: 42 Bond restraints: 5564 Sorted by residual: bond pdb=" C07 AJP A 505 " pdb=" C08 AJP A 505 " ideal model delta sigma weight residual 1.550 1.986 -0.436 2.00e-02 2.50e+03 4.76e+02 bond pdb=" C01 AJP A 505 " pdb=" C02 AJP A 505 " ideal model delta sigma weight residual 1.521 1.954 -0.433 2.00e-02 2.50e+03 4.69e+02 bond pdb=" C08 AJP A 505 " pdb=" O09 AJP A 505 " ideal model delta sigma weight residual 1.410 0.994 0.416 2.00e-02 2.50e+03 4.32e+02 bond pdb=" C05 AJP A 505 " pdb=" O09 AJP A 505 " ideal model delta sigma weight residual 1.407 1.798 -0.391 2.00e-02 2.50e+03 3.81e+02 bond pdb=" C02 AJP A 505 " pdb=" C03 AJP A 505 " ideal model delta sigma weight residual 1.525 1.138 0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.26: 105 105.26 - 112.92: 3090 112.92 - 120.57: 2411 120.57 - 128.23: 1909 128.23 - 135.89: 69 Bond angle restraints: 7584 Sorted by residual: angle pdb=" N54 OH6 A 501 " pdb=" C53 OH6 A 501 " pdb=" N58 OH6 A 501 " ideal model delta sigma weight residual 80.10 121.69 -41.59 3.00e+00 1.11e-01 1.92e+02 angle pdb=" C07 OH6 A 501 " pdb=" C08 OH6 A 501 " pdb=" C09 OH6 A 501 " ideal model delta sigma weight residual 152.67 121.20 31.47 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C52 OH6 A 501 " pdb=" C53 OH6 A 501 " pdb=" N58 OH6 A 501 " ideal model delta sigma weight residual 144.25 119.33 24.92 3.00e+00 1.11e-01 6.90e+01 angle pdb=" N SER A 381 " pdb=" CA SER A 381 " pdb=" C SER A 381 " ideal model delta sigma weight residual 113.17 104.12 9.05 1.26e+00 6.30e-01 5.16e+01 angle pdb=" N HIS A 382 " pdb=" CA HIS A 382 " pdb=" C HIS A 382 " ideal model delta sigma weight residual 109.96 118.89 -8.93 1.50e+00 4.44e-01 3.55e+01 ... (remaining 7579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 3047 33.71 - 67.42: 60 67.42 - 101.13: 11 101.13 - 134.84: 4 134.84 - 168.55: 2 Dihedral angle restraints: 3124 sinusoidal: 1217 harmonic: 1907 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual 180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" C33 OH6 A 501 " pdb=" O34 OH6 A 501 " pdb=" P35 OH6 A 501 " pdb=" O37 OH6 A 501 " ideal model delta sinusoidal sigma weight residual 213.23 44.68 168.55 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C01 OH6 A 501 " pdb=" C02 OH6 A 501 " pdb=" C03 OH6 A 501 " pdb=" C04 OH6 A 501 " ideal model delta sinusoidal sigma weight residual 185.44 28.07 157.37 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 3121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.101: 831 1.101 - 2.203: 0 2.203 - 3.304: 0 3.304 - 4.405: 2 4.405 - 5.507: 19 Chirality restraints: 852 Sorted by residual: chirality pdb=" C20 AJP A 505 " pdb=" C15 AJP A 505 " pdb=" C19 AJP A 505 " pdb=" C21 AJP A 505 " both_signs ideal model delta sigma weight residual False 2.96 -2.55 5.51 2.00e-01 2.50e+01 7.58e+02 chirality pdb=" C16 AJP A 505 " pdb=" C11 AJP A 505 " pdb=" C15 AJP A 505 " pdb=" C17 AJP A 505 " both_signs ideal model delta sigma weight residual False -2.70 2.74 -5.44 2.00e-01 2.50e+01 7.40e+02 chirality pdb=" C15 AJP A 505 " pdb=" C14 AJP A 505 " pdb=" C16 AJP A 505 " pdb=" C20 AJP A 505 " both_signs ideal model delta sigma weight residual False -2.42 2.93 -5.35 2.00e-01 2.50e+01 7.14e+02 ... (remaining 849 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 310 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ASN A 310 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN A 310 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 311 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 309 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ASN A 309 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN A 309 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 310 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 377 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 378 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.029 5.00e-02 4.00e+02 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 52 2.62 - 3.19: 4722 3.19 - 3.76: 8268 3.76 - 4.33: 11987 4.33 - 4.90: 20015 Nonbonded interactions: 45044 Sorted by model distance: nonbonded pdb=" O33 AJP A 505 " pdb=" O40 AJP A 505 " model vdw 2.051 2.440 nonbonded pdb=" O PHE A 340 " pdb=" ND1 HIS A 341 " model vdw 2.136 2.520 nonbonded pdb=" O VAL A 76 " pdb=" OG SER A 79 " model vdw 2.258 2.440 nonbonded pdb=" O GLY L 119 " pdb=" OG SER H 63 " model vdw 2.272 2.440 nonbonded pdb=" O42 AJP A 505 " pdb=" O43 AJP A 505 " model vdw 2.282 2.440 ... (remaining 45039 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 S 32 5.16 5 C 3550 2.51 5 N 869 2.21 5 O 945 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.000 Check model and map are aligned: 0.080 Process input model: 19.790 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.020 0.436 5564 Z= 1.297 Angle : 1.120 41.594 7584 Z= 0.472 Chirality : 0.781 5.507 852 Planarity : 0.005 0.053 900 Dihedral : 16.473 168.550 1897 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.18 (0.29), residues: 648 helix: -0.48 (0.26), residues: 330 sheet: -1.36 (0.41), residues: 119 loop : -3.00 (0.36), residues: 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.662 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3023 time to fit residues: 28.4240 Evaluate side-chains 68 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8584 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 91 HIS A 174 HIS A 315 ASN L 57 GLN L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5564 Z= 0.202 Angle : 1.126 35.555 7584 Z= 0.422 Chirality : 0.121 2.200 852 Planarity : 0.004 0.044 900 Dihedral : 13.546 139.892 774 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.79 (0.32), residues: 648 helix: 0.84 (0.28), residues: 325 sheet: -0.80 (0.44), residues: 120 loop : -2.59 (0.38), residues: 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.2649 time to fit residues: 20.7602 Evaluate side-chains 61 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0548 time to fit residues: 1.1170 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5564 Z= 0.178 Angle : 1.089 33.563 7584 Z= 0.406 Chirality : 0.123 2.166 852 Planarity : 0.004 0.044 900 Dihedral : 12.976 149.132 774 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.33), residues: 648 helix: 1.48 (0.29), residues: 325 sheet: -0.07 (0.48), residues: 110 loop : -2.24 (0.39), residues: 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.608 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.2744 time to fit residues: 21.1729 Evaluate side-chains 61 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8751 ------------------------------------------------------------------------------- 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: 4.9990 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5564 Z= 0.194 Angle : 1.087 32.882 7584 Z= 0.405 Chirality : 0.123 2.145 852 Planarity : 0.004 0.042 900 Dihedral : 12.515 149.900 774 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.36 (0.33), residues: 648 helix: 1.67 (0.29), residues: 325 sheet: -0.10 (0.47), residues: 120 loop : -1.95 (0.41), residues: 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.588 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 67 average time/residue: 0.2467 time to fit residues: 20.5239 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0495 time to fit residues: 0.8773 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5564 Z= 0.226 Angle : 1.092 32.411 7584 Z= 0.409 Chirality : 0.123 2.144 852 Planarity : 0.004 0.043 900 Dihedral : 12.237 151.190 774 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.44 (0.34), residues: 648 helix: 1.66 (0.29), residues: 325 sheet: 0.03 (0.47), residues: 119 loop : -1.83 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.612 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.2595 time to fit residues: 19.7944 Evaluate side-chains 62 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0558 time to fit residues: 0.9507 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5564 Z= 0.172 Angle : 1.076 32.035 7584 Z= 0.399 Chirality : 0.123 2.126 852 Planarity : 0.004 0.043 900 Dihedral : 11.665 147.994 774 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.68 (0.34), residues: 648 helix: 1.85 (0.29), residues: 324 sheet: 0.52 (0.51), residues: 108 loop : -1.84 (0.40), residues: 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.655 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.2402 time to fit residues: 18.8655 Evaluate side-chains 61 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9039 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 18 optimal weight: 2.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5564 Z= 0.191 Angle : 1.078 31.860 7584 Z= 0.401 Chirality : 0.123 2.126 852 Planarity : 0.004 0.043 900 Dihedral : 11.370 143.808 774 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.76 (0.34), residues: 648 helix: 1.89 (0.29), residues: 324 sheet: 0.58 (0.51), residues: 108 loop : -1.77 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.604 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.2483 time to fit residues: 19.8735 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0541 time to fit residues: 0.9386 ------------------------------------------------------------------------------- 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: 0.5980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 127 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 5564 Z= 0.161 Angle : 1.069 31.633 7584 Z= 0.395 Chirality : 0.123 2.120 852 Planarity : 0.004 0.043 900 Dihedral : 10.858 133.342 774 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.91 (0.34), residues: 648 helix: 2.02 (0.29), residues: 324 sheet: 0.72 (0.52), residues: 108 loop : -1.75 (0.41), residues: 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.597 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.2624 time to fit residues: 21.3894 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0549 time to fit residues: 0.9422 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 5564 Z= 0.148 Angle : 1.065 31.560 7584 Z= 0.393 Chirality : 0.123 2.116 852 Planarity : 0.004 0.042 900 Dihedral : 10.476 122.935 774 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.99 (0.34), residues: 648 helix: 2.11 (0.29), residues: 324 sheet: 0.66 (0.52), residues: 109 loop : -1.71 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.653 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2637 time to fit residues: 19.4013 Evaluate side-chains 59 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0712 time to fit residues: 1.0096 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 127 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5564 Z= 0.173 Angle : 1.071 31.605 7584 Z= 0.397 Chirality : 0.123 2.116 852 Planarity : 0.004 0.043 900 Dihedral : 10.362 114.619 774 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.00 (0.34), residues: 648 helix: 2.06 (0.29), residues: 325 sheet: 0.74 (0.53), residues: 108 loop : -1.65 (0.41), residues: 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.689 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2422 time to fit residues: 18.8893 Evaluate side-chains 62 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.0000 chunk 58 optimal weight: 0.8980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** L 96 ASN ** 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 = 0.3478 r_free = 0.3478 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101268 restraints weight = 5749.837| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.91 r_work: 0.2867 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 5564 Z= 0.136 Angle : 1.064 31.453 7584 Z= 0.393 Chirality : 0.123 2.111 852 Planarity : 0.003 0.043 900 Dihedral : 10.014 105.632 774 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.10 (0.35), residues: 648 helix: 2.15 (0.29), residues: 325 sheet: 0.72 (0.53), residues: 109 loop : -1.61 (0.41), residues: 214 =============================================================================== Job complete usr+sys time: 1552.80 seconds wall clock time: 28 minutes 56.28 seconds (1736.28 seconds total)