Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:50:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/11_2022/7n98_24252.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3625 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3625 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 22, 'TRANS': 450} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 2.59, per 1000 atoms: 0.71 Number of scatterers: 3625 At special positions: 0 Unit cell: (79.12, 71.38, 85.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 621 8.00 N 572 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 464 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 653.0 milliseconds 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 74.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.917A pdb=" N GLY A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 4.275A pdb=" N GLN A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 77 through 105 removed outlier: 3.712A pdb=" N ASP A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.724A pdb=" N SER A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.521A pdb=" N ILE A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 4.653A pdb=" N ILE A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.810A pdb=" N LEU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 179 through 209 removed outlier: 4.145A pdb=" N ASP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 266 removed outlier: 3.740A pdb=" N LEU A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.688A pdb=" N MET A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 323 removed outlier: 3.505A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.883A pdb=" N LEU A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.768A pdb=" N LEU A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 Proline residue: A 373 - end of helix removed outlier: 3.813A pdb=" N ALA A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.535A pdb=" N VAL A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.699A pdb=" N VAL A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 4.058A pdb=" N PHE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 493 removed outlier: 3.956A pdb=" N LYS A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 498 through 509 removed outlier: 4.732A pdb=" N LYS A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218 214 hydrogen bonds defined for protein. 642 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: 0.90 Time building geometry restraints manager: 1.81 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: 1088 1.34 - 1.46: 750 1.46 - 1.58: 1857 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3725 Sorted by residual: bond pdb=" N LYS A 440 " pdb=" CA LYS A 440 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.25e+00 bond pdb=" N ALA A 53 " pdb=" CA ALA A 53 " ideal model delta sigma weight residual 1.463 1.456 0.007 6.90e-03 2.10e+04 1.16e+00 bond pdb=" C GLY A 52 " pdb=" N ALA A 53 " ideal model delta sigma weight residual 1.341 1.323 0.017 1.65e-02 3.67e+03 1.09e+00 bond pdb=" C VAL A 135 " pdb=" N PRO A 136 " ideal model delta sigma weight residual 1.332 1.324 0.008 8.20e-03 1.49e+04 1.01e+00 bond pdb=" N PRO A 136 " pdb=" CA PRO A 136 " ideal model delta sigma weight residual 1.473 1.465 0.008 8.50e-03 1.38e+04 8.95e-01 ... (remaining 3720 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.80: 112 106.80 - 113.63: 2035 113.63 - 120.46: 1577 120.46 - 127.29: 1317 127.29 - 134.11: 42 Bond angle restraints: 5083 Sorted by residual: angle pdb=" N VAL A 372 " pdb=" CA VAL A 372 " pdb=" C VAL A 372 " ideal model delta sigma weight residual 108.88 115.75 -6.87 2.16e+00 2.14e-01 1.01e+01 angle pdb=" C MET A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta sigma weight residual 120.09 123.82 -3.73 1.25e+00 6.40e-01 8.89e+00 angle pdb=" C GLY A 52 " pdb=" N ALA A 53 " pdb=" CA ALA A 53 " ideal model delta sigma weight residual 119.83 122.80 -2.97 1.11e+00 8.12e-01 7.16e+00 angle pdb=" N LYS A 440 " pdb=" CA LYS A 440 " pdb=" C LYS A 440 " ideal model delta sigma weight residual 111.28 108.53 2.75 1.09e+00 8.42e-01 6.39e+00 angle pdb=" C ALA A 53 " pdb=" CA ALA A 53 " pdb=" CB ALA A 53 " ideal model delta sigma weight residual 113.57 109.70 3.87 1.57e+00 4.06e-01 6.09e+00 ... (remaining 5078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 1934 15.76 - 31.52: 165 31.52 - 47.28: 43 47.28 - 63.04: 11 63.04 - 78.81: 4 Dihedral angle restraints: 2157 sinusoidal: 780 harmonic: 1377 Sorted by residual: dihedral pdb=" CA GLU A 382 " pdb=" C GLU A 382 " pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL A 372 " pdb=" C VAL A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ALA A 53 " pdb=" C ALA A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 407 0.041 - 0.082: 143 0.082 - 0.123: 41 0.123 - 0.164: 5 0.164 - 0.205: 2 Chirality restraints: 598 Sorted by residual: chirality pdb=" CB ILE A 486 " pdb=" CA ILE A 486 " pdb=" CG1 ILE A 486 " pdb=" CG2 ILE A 486 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 54 " pdb=" N PRO A 54 " pdb=" C PRO A 54 " pdb=" CB PRO A 54 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA PRO A 425 " pdb=" N PRO A 425 " pdb=" C PRO A 425 " pdb=" CB PRO A 425 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 595 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 466 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO A 467 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 53 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 54 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 496 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 497 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " 0.027 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 584 2.75 - 3.29: 3814 3.29 - 3.83: 5785 3.83 - 4.36: 6120 4.36 - 4.90: 10383 Nonbonded interactions: 26686 Sorted by model distance: nonbonded pdb=" CE MET A 409 " pdb=" CD2 LEU A 495 " model vdw 2.217 3.880 nonbonded pdb=" O PHE A 358 " pdb=" OG1 THR A 362 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASN A 318 " pdb=" OG SER A 450 " model vdw 2.300 2.440 nonbonded pdb=" O ILE A 176 " pdb=" OG SER A 177 " model vdw 2.336 2.440 nonbonded pdb=" OE2 GLU A 500 " pdb=" NH2 ARG A 503 " model vdw 2.337 2.520 ... (remaining 26681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2412 2.51 5 N 572 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 2.990 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3725 Z= 0.267 Angle : 0.720 6.867 5083 Z= 0.403 Chirality : 0.046 0.205 598 Planarity : 0.006 0.064 627 Dihedral : 13.694 78.806 1266 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 0.27 % 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: -1.56 (0.40), residues: 471 helix: -0.05 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -3.04 (0.50), residues: 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.430 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1215 time to fit residues: 16.0043 Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3725 Z= 0.207 Angle : 0.647 8.804 5083 Z= 0.333 Chirality : 0.044 0.162 598 Planarity : 0.005 0.055 627 Dihedral : 4.942 24.024 501 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 1.07 % 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: -1.05 (0.41), residues: 471 helix: 0.38 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -3.06 (0.51), residues: 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.452 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 91 average time/residue: 0.1175 time to fit residues: 14.1381 Evaluate side-chains 87 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0435 time to fit residues: 0.8906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.8177 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3725 Z= 0.216 Angle : 0.609 6.639 5083 Z= 0.315 Chirality : 0.044 0.176 598 Planarity : 0.005 0.052 627 Dihedral : 4.802 22.752 501 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 1.88 % 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: -0.87 (0.41), residues: 471 helix: 0.52 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -3.03 (0.51), residues: 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.433 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.1094 time to fit residues: 13.3870 Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0372 time to fit residues: 0.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3725 Z= 0.185 Angle : 0.589 6.475 5083 Z= 0.302 Chirality : 0.043 0.168 598 Planarity : 0.005 0.055 627 Dihedral : 4.618 22.882 501 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 1.61 % 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: -0.67 (0.41), residues: 471 helix: 0.67 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.94 (0.52), residues: 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 0.1051 time to fit residues: 13.8099 Evaluate side-chains 86 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0376 time to fit residues: 0.7580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 31 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3725 Z= 0.183 Angle : 0.592 6.437 5083 Z= 0.302 Chirality : 0.043 0.189 598 Planarity : 0.005 0.051 627 Dihedral : 4.483 22.368 501 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 2.14 % 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: -0.49 (0.41), residues: 471 helix: 0.79 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.88 (0.53), residues: 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.441 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 98 average time/residue: 0.0938 time to fit residues: 12.7265 Evaluate side-chains 89 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0495 time to fit residues: 0.9645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3725 Z= 0.177 Angle : 0.577 6.226 5083 Z= 0.293 Chirality : 0.043 0.164 598 Planarity : 0.005 0.053 627 Dihedral : 4.390 22.303 501 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.61 % 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: -0.39 (0.41), residues: 471 helix: 0.87 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.85 (0.53), residues: 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 90 average time/residue: 0.0927 time to fit residues: 11.6461 Evaluate side-chains 89 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3725 Z= 0.182 Angle : 0.586 6.332 5083 Z= 0.295 Chirality : 0.043 0.191 598 Planarity : 0.005 0.052 627 Dihedral : 4.355 22.801 501 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 1.61 % 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: -0.31 (0.41), residues: 471 helix: 0.94 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.87 (0.53), residues: 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.417 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 0.0962 time to fit residues: 12.4394 Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0430 time to fit residues: 0.8231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.0670 chunk 43 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3725 Z= 0.171 Angle : 0.589 7.017 5083 Z= 0.296 Chirality : 0.043 0.165 598 Planarity : 0.005 0.053 627 Dihedral : 4.314 22.589 501 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.07 % 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: -0.17 (0.41), residues: 471 helix: 1.05 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.83 (0.52), residues: 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 94 average time/residue: 0.0869 time to fit residues: 11.2737 Evaluate side-chains 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0439 time to fit residues: 0.8114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3725 Z= 0.194 Angle : 0.618 10.409 5083 Z= 0.308 Chirality : 0.043 0.191 598 Planarity : 0.005 0.052 627 Dihedral : 4.328 22.486 501 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 1.07 % 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: -0.16 (0.41), residues: 471 helix: 1.07 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.87 (0.53), residues: 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 94 average time/residue: 0.1087 time to fit residues: 13.8750 Evaluate side-chains 88 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0416 time to fit residues: 0.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 34 optimal weight: 0.0030 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3725 Z= 0.172 Angle : 0.635 12.398 5083 Z= 0.310 Chirality : 0.043 0.215 598 Planarity : 0.005 0.052 627 Dihedral : 4.301 22.339 501 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 0.00 % 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: -0.06 (0.41), residues: 471 helix: 1.13 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.81 (0.53), residues: 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1042 time to fit residues: 13.2432 Evaluate side-chains 90 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103046 restraints weight = 6958.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106634 restraints weight = 3714.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109126 restraints weight = 2422.207| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 3725 Z= 0.185 Angle : 0.618 12.231 5083 Z= 0.305 Chirality : 0.042 0.151 598 Planarity : 0.005 0.052 627 Dihedral : 4.281 22.219 501 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 0.54 % 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: 0.07 (0.41), residues: 471 helix: 1.25 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.67 (0.53), residues: 152 =============================================================================== Job complete usr+sys time: 1028.28 seconds wall clock time: 20 minutes 8.22 seconds (1208.22 seconds total)