Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 02:51:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/10_2023/8grs_34214_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 3411 2.51 5 N 821 2.21 5 O 884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5148 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5148 Unusual residues: {'POV': 1} Classifications: {'peptide': 626, 'undetermined': 1} Link IDs: {'PTRANS': 22, 'TRANS': 603, None: 1} Not linked: pdbres="GLY A 718 " pdbres="POV A 901 " Chain breaks: 4 Time building chain proxies: 3.31, per 1000 atoms: 0.64 Number of scatterers: 5148 At special positions: 0 Unit cell: (95.12, 82.82, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 884 8.00 N 821 7.00 C 3411 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 - 3.50 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 650.5 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 59.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.662A pdb=" N ARG A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 4.156A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 191 through 216 removed outlier: 3.694A pdb=" N HIS A 196 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 201 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 210 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 213 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 269 through 288 removed outlier: 4.338A pdb=" N ASN A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 349 removed outlier: 4.035A pdb=" N LYS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 415 through 445 Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 467 through 490 removed outlier: 3.799A pdb=" N LEU A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 495 through 533 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 554 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 6.160A pdb=" N LEU A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 627 removed outlier: 4.121A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.554A pdb=" N ILE A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 688 removed outlier: 3.571A pdb=" N PHE A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Proline residue: A 675 - end of helix Processing helix chain 'A' and resid 695 through 716 255 hydrogen bonds defined for protein. 708 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: 1.33 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 763 1.27 - 1.41: 1434 1.41 - 1.54: 3010 1.54 - 1.67: 30 1.67 - 1.81: 46 Bond restraints: 5283 Sorted by residual: bond pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 1.524 1.399 0.126 1.16e-02 7.43e+03 1.17e+02 bond pdb=" C VAL A 153 " pdb=" O VAL A 153 " ideal model delta sigma weight residual 1.236 1.138 0.099 1.11e-02 8.12e+03 7.94e+01 bond pdb=" CA ALA A 562 " pdb=" C ALA A 562 " ideal model delta sigma weight residual 1.524 1.416 0.108 1.28e-02 6.10e+03 7.12e+01 bond pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.34e-02 5.57e+03 6.35e+01 bond pdb=" CA PHE A 512 " pdb=" C PHE A 512 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.34e-02 5.57e+03 6.18e+01 ... (remaining 5278 not shown) Histogram of bond angle deviations from ideal: 93.35 - 101.58: 42 101.58 - 109.81: 1073 109.81 - 118.04: 2884 118.04 - 126.27: 3076 126.27 - 134.51: 88 Bond angle restraints: 7163 Sorted by residual: angle pdb=" C ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta sigma weight residual 111.70 93.35 18.35 1.28e+00 6.10e-01 2.06e+02 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 110.23 96.00 14.23 1.04e+00 9.25e-01 1.87e+02 angle pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" C GLU A 134 " ideal model delta sigma weight residual 114.56 97.71 16.85 1.27e+00 6.20e-01 1.76e+02 angle pdb=" C LEU A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 119.05 105.94 13.11 1.11e+00 8.12e-01 1.40e+02 angle pdb=" C ALA A 674 " pdb=" N PRO A 675 " pdb=" CA PRO A 675 " ideal model delta sigma weight residual 119.32 106.81 12.51 1.14e+00 7.69e-01 1.21e+02 ... (remaining 7158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 2416 21.14 - 42.27: 372 42.27 - 63.41: 282 63.41 - 84.54: 15 84.54 - 105.68: 5 Dihedral angle restraints: 3090 sinusoidal: 1243 harmonic: 1847 Sorted by residual: dihedral pdb=" C ILE A 511 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta harmonic sigma weight residual -122.00 -97.70 -24.30 0 2.50e+00 1.60e-01 9.45e+01 dihedral pdb=" C VAL A 244 " pdb=" N VAL A 244 " pdb=" CA VAL A 244 " pdb=" CB VAL A 244 " ideal model delta harmonic sigma weight residual -122.00 -134.63 12.63 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C ILE A 183 " pdb=" N ILE A 183 " pdb=" CA ILE A 183 " pdb=" CB ILE A 183 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 3087 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.111: 572 0.111 - 0.222: 176 0.222 - 0.333: 44 0.333 - 0.443: 16 0.443 - 0.554: 7 Chirality restraints: 815 Sorted by residual: chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA LEU A 517 " pdb=" N LEU A 517 " pdb=" C LEU A 517 " pdb=" CB LEU A 517 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ALA A 267 " pdb=" N ALA A 267 " pdb=" C ALA A 267 " pdb=" CB ALA A 267 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 812 not shown) Planarity restraints: 869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 517 " 0.132 5.00e-02 4.00e+02 2.01e-01 6.48e+01 pdb=" N PRO A 518 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.101 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.115 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 162 " 0.120 5.00e-02 4.00e+02 1.78e-01 5.06e+01 pdb=" N PRO A 163 " -0.307 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.103 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 674 " 0.117 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO A 675 " -0.293 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.102 5.00e-02 4.00e+02 ... (remaining 866 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 2 2.01 - 2.73: 1139 2.73 - 3.45: 7288 3.45 - 4.18: 13516 4.18 - 4.90: 21986 Nonbonded interactions: 43931 Sorted by model distance: nonbonded pdb=" NH2 ARG A 249 " pdb=" OH TYR A 264 " model vdw 1.285 2.520 nonbonded pdb=" OG1 THR A 284 " pdb=" CB LEU A 331 " model vdw 1.475 3.440 nonbonded pdb=" OG1 THR A 284 " pdb=" CA LEU A 331 " model vdw 2.012 3.470 nonbonded pdb=" O PHE A 512 " pdb=" O MET A 513 " model vdw 2.265 3.040 nonbonded pdb=" N GLU A 134 " pdb=" N ASP A 135 " model vdw 2.273 2.560 ... (remaining 43926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 7.030 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.770 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.016 0.128 5283 Z= 1.033 Angle : 1.944 18.350 7163 Z= 1.326 Chirality : 0.128 0.554 815 Planarity : 0.015 0.201 869 Dihedral : 26.294 105.676 1892 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 5.84 % Allowed : 21.27 % Favored : 72.89 % Rotamer: Outliers : 44.03 % Allowed : 14.44 % Favored : 41.53 % Cbeta Deviations : 1.00 % 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: -5.46 (0.26), residues: 616 helix: -2.81 (0.20), residues: 384 sheet: -5.55 (0.90), residues: 15 loop : -4.85 (0.34), residues: 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 177 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 82 residues processed: 334 average time/residue: 0.2029 time to fit residues: 83.5565 Evaluate side-chains 220 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 138 time to evaluate : 0.560 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 4 residues processed: 82 average time/residue: 0.0820 time to fit residues: 10.9872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 43 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5283 Z= 0.304 Angle : 0.858 9.332 7163 Z= 0.443 Chirality : 0.048 0.202 815 Planarity : 0.009 0.105 869 Dihedral : 9.752 77.264 712 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 1.30 % Allowed : 15.91 % Favored : 82.79 % Rotamer: Outliers : 6.42 % Allowed : 27.81 % Favored : 65.78 % 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: -3.41 (0.32), residues: 616 helix: -1.01 (0.24), residues: 376 sheet: -5.19 (1.08), residues: 10 loop : -4.32 (0.38), residues: 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 176 average time/residue: 0.1633 time to fit residues: 37.0622 Evaluate side-chains 141 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.0761 time to fit residues: 3.1205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5283 Z= 0.246 Angle : 0.746 10.921 7163 Z= 0.380 Chirality : 0.043 0.162 815 Planarity : 0.007 0.091 869 Dihedral : 8.894 75.267 712 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.65 % Allowed : 15.42 % Favored : 83.93 % Rotamer: Outliers : 3.74 % Allowed : 32.26 % Favored : 63.99 % 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: -2.50 (0.33), residues: 616 helix: -0.26 (0.25), residues: 374 sheet: -3.17 (1.63), residues: 10 loop : -4.07 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 0.1880 time to fit residues: 33.8900 Evaluate side-chains 125 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0539 time to fit residues: 1.7883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5283 Z= 0.232 Angle : 0.704 9.146 7163 Z= 0.356 Chirality : 0.042 0.149 815 Planarity : 0.007 0.086 869 Dihedral : 8.535 72.366 712 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.64 % Favored : 86.04 % Rotamer: Outliers : 3.74 % Allowed : 32.26 % Favored : 63.99 % 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: -2.04 (0.34), residues: 616 helix: 0.10 (0.26), residues: 376 sheet: -2.44 (1.87), residues: 10 loop : -3.93 (0.39), residues: 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 0.1718 time to fit residues: 30.3471 Evaluate side-chains 118 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0604 time to fit residues: 1.7327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5283 Z= 0.316 Angle : 0.748 8.717 7163 Z= 0.375 Chirality : 0.043 0.145 815 Planarity : 0.007 0.088 869 Dihedral : 8.611 69.600 712 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.96 % Favored : 85.55 % Rotamer: Outliers : 4.28 % Allowed : 31.55 % Favored : 64.17 % 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 (0.34), residues: 616 helix: 0.27 (0.26), residues: 366 sheet: -2.27 (1.97), residues: 10 loop : -3.60 (0.40), residues: 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 0.1846 time to fit residues: 29.8556 Evaluate side-chains 121 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0539 time to fit residues: 2.0850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5283 Z= 0.226 Angle : 0.673 8.287 7163 Z= 0.337 Chirality : 0.041 0.141 815 Planarity : 0.007 0.084 869 Dihedral : 8.390 64.083 712 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.31 % Favored : 86.20 % Rotamer: Outliers : 2.50 % Allowed : 31.55 % Favored : 65.95 % 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: -1.50 (0.35), residues: 616 helix: 0.57 (0.27), residues: 364 sheet: -1.98 (2.10), residues: 10 loop : -3.57 (0.39), residues: 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 123 average time/residue: 0.1716 time to fit residues: 27.1156 Evaluate side-chains 115 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0526 time to fit residues: 1.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5283 Z= 0.222 Angle : 0.679 8.234 7163 Z= 0.337 Chirality : 0.041 0.141 815 Planarity : 0.006 0.082 869 Dihedral : 8.237 62.424 712 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.66 % Favored : 86.85 % Rotamer: Outliers : 2.50 % Allowed : 31.91 % Favored : 65.60 % 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: -1.28 (0.35), residues: 616 helix: 0.74 (0.27), residues: 364 sheet: -1.64 (2.19), residues: 10 loop : -3.50 (0.40), residues: 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.1755 time to fit residues: 26.6694 Evaluate side-chains 119 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0528 time to fit residues: 1.5933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 46 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5283 Z= 0.214 Angle : 0.682 8.098 7163 Z= 0.337 Chirality : 0.041 0.177 815 Planarity : 0.007 0.078 869 Dihedral : 7.916 59.562 712 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.99 % Favored : 86.69 % Rotamer: Outliers : 1.60 % Allowed : 32.26 % Favored : 66.13 % 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: -1.21 (0.36), residues: 616 helix: 0.76 (0.27), residues: 364 sheet: -1.82 (2.16), residues: 10 loop : -3.37 (0.41), residues: 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 0.1846 time to fit residues: 28.5493 Evaluate side-chains 107 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0663 time to fit residues: 1.0800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5283 Z= 0.272 Angle : 0.713 9.146 7163 Z= 0.354 Chirality : 0.042 0.171 815 Planarity : 0.007 0.079 869 Dihedral : 7.556 58.337 712 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.66 % Favored : 86.85 % Rotamer: Outliers : 1.96 % Allowed : 33.51 % Favored : 64.53 % 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: -1.28 (0.35), residues: 616 helix: 0.66 (0.27), residues: 363 sheet: -1.48 (2.29), residues: 10 loop : -3.32 (0.41), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.1573 time to fit residues: 23.6245 Evaluate side-chains 114 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0740 time to fit residues: 1.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.0040 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5283 Z= 0.204 Angle : 0.709 8.401 7163 Z= 0.351 Chirality : 0.041 0.207 815 Planarity : 0.006 0.074 869 Dihedral : 7.208 52.496 712 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.36 % Favored : 88.15 % Rotamer: Outliers : 0.71 % Allowed : 34.58 % Favored : 64.71 % 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: -1.26 (0.35), residues: 616 helix: 0.68 (0.27), residues: 367 sheet: -1.41 (2.31), residues: 10 loop : -3.40 (0.41), residues: 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.1665 time to fit residues: 25.5649 Evaluate side-chains 112 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2041 time to fit residues: 1.5530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118671 restraints weight = 6977.358| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.95 r_work: 0.3301 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5283 Z= 0.288 Angle : 0.761 11.566 7163 Z= 0.376 Chirality : 0.044 0.208 815 Planarity : 0.007 0.077 869 Dihedral : 7.206 55.439 712 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.66 % Favored : 86.85 % Rotamer: Outliers : 0.71 % Allowed : 34.40 % Favored : 64.88 % 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: -1.33 (0.35), residues: 616 helix: 0.67 (0.27), residues: 365 sheet: -2.27 (2.06), residues: 10 loop : -3.45 (0.40), residues: 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.53 seconds wall clock time: 30 minutes 58.13 seconds (1858.13 seconds total)