Starting phenix.real_space_refine on Fri Dec 27 23:46:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.map" model { file = "/net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odf_12827/12_2024/7odf_12827.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ni 1 6.56 5 Zn 1 6.06 5 P 78 5.49 5 S 16 5.16 5 C 4068 2.51 5 N 1216 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6847 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5205 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 30, 'TRANS': 672} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 15, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 256 Chain: "E" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 919 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 36} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NI': 1, ' ZN': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4879 SG CYS A 680 72.409 39.562 72.141 1.00106.49 S ATOM 4900 SG CYS A 683 76.785 37.518 72.841 1.00112.67 S ATOM 5015 SG CYS A 701 74.842 39.676 74.908 1.00117.90 S Time building chain proxies: 4.98, per 1000 atoms: 0.73 Number of scatterers: 6847 At special positions: 0 Unit cell: (84.864, 98.176, 115.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ni 1 28.00 S 16 16.00 P 78 15.00 O 1467 8.00 N 1216 7.00 C 4068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 633.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 701 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 683 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 680 " 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 50.2% alpha, 8.1% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.779A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 removed outlier: 3.631A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.571A pdb=" N SER A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 121 through 160 removed outlier: 3.593A pdb=" N THR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.618A pdb=" N GLU A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 501 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.529A pdb=" N SER A 512 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 513 " --> pdb=" O TRP A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 561 through 579 Processing helix chain 'A' and resid 580 through 608 removed outlier: 3.795A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.588A pdb=" N PHE A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 710 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.238A pdb=" N ASN A 61 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 330 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 65 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP A 328 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 442 removed outlier: 3.538A pdb=" N VAL A 407 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 408 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 616 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 410 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU A 618 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N VAL A 412 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 667 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AA4, first strand: chain 'A' and resid 695 through 697 269 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.00 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: 1905 1.34 - 1.46: 1707 1.46 - 1.58: 3356 1.58 - 1.70: 152 1.70 - 1.82: 22 Bond restraints: 7142 Sorted by residual: bond pdb=" O3' DG C 1 " pdb=" P DG C 2 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.50e-02 4.44e+03 3.71e+00 bond pdb=" CG LEU A 336 " pdb=" CD1 LEU A 336 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CD GLU A 591 " pdb=" OE1 GLU A 591 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.31e+00 bond pdb=" CG GLU A 591 " pdb=" CD GLU A 591 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.09e-01 bond pdb=" O4' DC E 14 " pdb=" C1' DC E 14 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 7.80e-01 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9786 1.27 - 2.53: 217 2.53 - 3.80: 41 3.80 - 5.06: 8 5.06 - 6.33: 4 Bond angle restraints: 10056 Sorted by residual: angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.22 114.61 -4.39 1.54e+00 4.22e-01 8.13e+00 angle pdb=" O3' DG C 2 " pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 111.50 108.21 3.29 1.50e+00 4.44e-01 4.82e+00 angle pdb=" CB MET A 25 " pdb=" CG MET A 25 " pdb=" SD MET A 25 " ideal model delta sigma weight residual 112.70 119.03 -6.33 3.00e+00 1.11e-01 4.45e+00 angle pdb=" CB ARG A 41 " pdb=" CG ARG A 41 " pdb=" CD ARG A 41 " ideal model delta sigma weight residual 111.30 116.04 -4.74 2.30e+00 1.89e-01 4.24e+00 angle pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " pdb=" CG GLU A 591 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.22e+00 ... (remaining 10051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 3964 34.02 - 68.03: 241 68.03 - 102.05: 16 102.05 - 136.06: 2 136.06 - 170.08: 2 Dihedral angle restraints: 4225 sinusoidal: 2177 harmonic: 2048 Sorted by residual: dihedral pdb=" O4' U F 3 " pdb=" C1' U F 3 " pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sinusoidal sigma weight residual 200.00 29.92 170.08 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U F 44 " pdb=" C1' U F 44 " pdb=" N1 U F 44 " pdb=" C2 U F 44 " ideal model delta sinusoidal sigma weight residual -160.00 -103.50 -56.50 1 1.50e+01 4.44e-03 1.91e+01 dihedral pdb=" C4' DT E 11 " pdb=" C3' DT E 11 " pdb=" O3' DT E 11 " pdb=" P DA E 12 " ideal model delta sinusoidal sigma weight residual 220.00 79.58 140.42 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 4222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 802 0.031 - 0.062: 273 0.062 - 0.092: 64 0.092 - 0.123: 38 0.123 - 0.154: 8 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA GLU A 591 " pdb=" N GLU A 591 " pdb=" C GLU A 591 " pdb=" CB GLU A 591 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA LYS A 625 " pdb=" N LYS A 625 " pdb=" C LYS A 625 " pdb=" CB LYS A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1182 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 587 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C LYS A 587 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 587 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 588 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 218 " 0.013 2.00e-02 2.50e+03 1.44e-02 4.13e+00 pdb=" CG TYR A 218 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 218 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 218 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 218 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 218 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 218 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 218 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 337 " -0.016 2.00e-02 2.50e+03 1.24e-02 3.09e+00 pdb=" CG TYR A 337 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 337 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 337 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 337 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 337 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 337 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 337 " 0.001 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 32 2.54 - 3.13: 5116 3.13 - 3.72: 11540 3.72 - 4.31: 16290 4.31 - 4.90: 25151 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASP A 413 " pdb="NI NI A 801 " model vdw 1.952 2.180 nonbonded pdb=" OG1 THR A 60 " pdb=" O VAL A 372 " model vdw 2.198 3.040 nonbonded pdb=" O ASN A 275 " pdb=" O2' G F 14 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 296 " pdb=" OP2 C F 19 " model vdw 2.239 3.040 nonbonded pdb=" O LYS A 400 " pdb=" OG SER A 403 " model vdw 2.336 3.040 ... (remaining 58124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.000 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7142 Z= 0.207 Angle : 0.490 6.331 10056 Z= 0.265 Chirality : 0.037 0.154 1185 Planarity : 0.003 0.032 1014 Dihedral : 19.381 170.081 2901 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.32), residues: 699 helix: 2.00 (0.29), residues: 315 sheet: 0.19 (0.61), residues: 70 loop : 0.20 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 636 HIS 0.002 0.001 HIS A 293 PHE 0.020 0.001 PHE A 341 TYR 0.033 0.002 TYR A 218 ARG 0.005 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.591 Fit side-chains REVERT: A 621 ASP cc_start: 0.7918 (t70) cc_final: 0.7329 (t70) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.1961 time to fit residues: 93.9189 Evaluate side-chains 46 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0870 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7142 Z= 0.148 Angle : 0.507 7.227 10056 Z= 0.270 Chirality : 0.037 0.151 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.030 168.997 1811 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.37 % Allowed : 7.05 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.32), residues: 699 helix: 2.42 (0.29), residues: 312 sheet: -0.21 (0.57), residues: 82 loop : 0.31 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 636 HIS 0.004 0.001 HIS A 293 PHE 0.014 0.001 PHE A 488 TYR 0.019 0.001 TYR A 218 ARG 0.003 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.718 Fit side-chains REVERT: A 621 ASP cc_start: 0.7809 (t70) cc_final: 0.7384 (t70) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.0248 time to fit residues: 63.7223 Evaluate side-chains 48 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7142 Z= 0.321 Angle : 0.540 5.794 10056 Z= 0.289 Chirality : 0.040 0.158 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.105 172.178 1811 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.37 % Allowed : 10.57 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 699 helix: 2.28 (0.29), residues: 312 sheet: 0.02 (0.63), residues: 74 loop : 0.36 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 PHE 0.014 0.001 PHE A 488 TYR 0.027 0.002 TYR A 218 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.696 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 1.0544 time to fit residues: 64.4680 Evaluate side-chains 51 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7142 Z= 0.194 Angle : 0.484 6.499 10056 Z= 0.259 Chirality : 0.037 0.136 1185 Planarity : 0.003 0.030 1014 Dihedral : 21.009 171.055 1811 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.15 % Allowed : 10.76 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.32), residues: 699 helix: 2.31 (0.29), residues: 316 sheet: -0.43 (0.59), residues: 82 loop : 0.32 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 PHE 0.013 0.001 PHE A 488 TYR 0.021 0.001 TYR A 218 ARG 0.007 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.7870 (t70) cc_final: 0.7480 (t70) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.9716 time to fit residues: 61.5852 Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7142 Z= 0.163 Angle : 0.467 7.253 10056 Z= 0.250 Chirality : 0.036 0.159 1185 Planarity : 0.003 0.031 1014 Dihedral : 20.930 170.456 1811 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.54 % Allowed : 11.74 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.32), residues: 699 helix: 2.45 (0.29), residues: 315 sheet: -0.47 (0.58), residues: 82 loop : 0.34 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 636 HIS 0.003 0.000 HIS A 293 PHE 0.010 0.001 PHE A 640 TYR 0.026 0.001 TYR A 218 ARG 0.006 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 391 ARG cc_start: 0.8524 (ptp-170) cc_final: 0.8315 (ptp-170) REVERT: A 513 MET cc_start: 0.7692 (mmt) cc_final: 0.7373 (mmt) REVERT: A 610 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 621 ASP cc_start: 0.7848 (t70) cc_final: 0.7426 (t70) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.7951 time to fit residues: 53.0088 Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7142 Z= 0.301 Angle : 0.517 7.016 10056 Z= 0.274 Chirality : 0.039 0.133 1185 Planarity : 0.003 0.033 1014 Dihedral : 21.035 172.667 1811 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.13 % Allowed : 11.94 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.32), residues: 699 helix: 2.46 (0.29), residues: 309 sheet: -0.19 (0.61), residues: 74 loop : 0.36 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 PHE 0.010 0.001 PHE A 640 TYR 0.031 0.002 TYR A 218 ARG 0.004 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 513 MET cc_start: 0.7800 (mmt) cc_final: 0.7582 (mmt) REVERT: A 610 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8188 (tp) REVERT: A 621 ASP cc_start: 0.7901 (t70) cc_final: 0.7476 (t70) outliers start: 16 outliers final: 11 residues processed: 60 average time/residue: 0.9927 time to fit residues: 64.0594 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 61 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7142 Z= 0.162 Angle : 0.483 8.585 10056 Z= 0.254 Chirality : 0.037 0.136 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.015 171.909 1811 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.35 % Allowed : 12.52 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.32), residues: 699 helix: 2.52 (0.29), residues: 309 sheet: -0.29 (0.61), residues: 72 loop : 0.41 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 636 HIS 0.002 0.001 HIS A 293 PHE 0.012 0.001 PHE A 488 TYR 0.026 0.001 TYR A 218 ARG 0.005 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 513 MET cc_start: 0.7758 (mmt) cc_final: 0.7477 (mmt) REVERT: A 610 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8138 (tp) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.9034 time to fit residues: 53.7554 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7142 Z= 0.217 Angle : 0.495 7.939 10056 Z= 0.260 Chirality : 0.037 0.132 1185 Planarity : 0.003 0.031 1014 Dihedral : 20.976 172.944 1811 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.35 % Allowed : 13.31 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 699 helix: 2.42 (0.29), residues: 315 sheet: -0.26 (0.61), residues: 74 loop : 0.35 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 PHE 0.014 0.001 PHE A 341 TYR 0.032 0.001 TYR A 218 ARG 0.003 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 513 MET cc_start: 0.7807 (mmt) cc_final: 0.7503 (mmt) REVERT: A 610 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8180 (tp) REVERT: A 621 ASP cc_start: 0.7906 (t70) cc_final: 0.7436 (t70) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 1.0008 time to fit residues: 62.6829 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7142 Z= 0.277 Angle : 0.524 9.312 10056 Z= 0.274 Chirality : 0.038 0.132 1185 Planarity : 0.003 0.037 1014 Dihedral : 21.047 174.542 1811 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 13.11 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.32), residues: 699 helix: 2.36 (0.29), residues: 315 sheet: -0.46 (0.57), residues: 80 loop : 0.38 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 PHE 0.013 0.001 PHE A 341 TYR 0.035 0.002 TYR A 218 ARG 0.009 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8211 (tp) outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 0.8964 time to fit residues: 57.2544 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7142 Z= 0.216 Angle : 0.508 7.924 10056 Z= 0.267 Chirality : 0.038 0.165 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.038 174.595 1811 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.54 % Allowed : 13.89 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.32), residues: 699 helix: 2.38 (0.29), residues: 315 sheet: -0.50 (0.57), residues: 80 loop : 0.39 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 PHE 0.014 0.001 PHE A 488 TYR 0.035 0.002 TYR A 218 ARG 0.008 0.000 ARG A 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 513 MET cc_start: 0.7795 (mmt) cc_final: 0.7547 (mmt) REVERT: A 610 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 621 ASP cc_start: 0.7922 (t70) cc_final: 0.7478 (t70) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 0.9222 time to fit residues: 55.6906 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104963 restraints weight = 9259.044| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.10 r_work: 0.3237 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7142 Z= 0.180 Angle : 0.507 10.785 10056 Z= 0.263 Chirality : 0.037 0.169 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.020 174.531 1811 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.15 % Allowed : 14.09 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 699 helix: 2.39 (0.29), residues: 315 sheet: -0.54 (0.57), residues: 80 loop : 0.40 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 PHE 0.011 0.001 PHE A 341 TYR 0.037 0.001 TYR A 218 ARG 0.006 0.000 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.34 seconds wall clock time: 41 minutes 18.43 seconds (2478.43 seconds total)