Starting phenix.real_space_refine on Mon Sep 23 15:51:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/09_2024/7n98_24252.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/09_2024/7n98_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_24252/09_2024/7n98_24252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/09_2024/7n98_24252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/09_2024/7n98_24252.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n98_24252/09_2024/7n98_24252.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.34, per 1000 atoms: 0.92 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 488.5 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: 0.35 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: 0.89 Time building geometry restraints manager: 1.08 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: 0.00 - 1.37: 4806 1.37 - 2.75: 222 2.75 - 4.12: 34 4.12 - 5.49: 19 5.49 - 6.87: 2 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 3.040 nonbonded pdb=" OD1 ASN A 318 " pdb=" OG SER A 450 " model vdw 2.300 3.040 nonbonded pdb=" O ILE A 176 " pdb=" OG SER A 177 " model vdw 2.336 3.040 nonbonded pdb=" OE2 GLU A 500 " pdb=" NH2 ARG A 503 " model vdw 2.337 3.120 ... (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 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 % Allowed : 0.54 % Favored : 99.20 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 407 HIS 0.002 0.001 HIS A 423 PHE 0.016 0.002 PHE A 285 TYR 0.013 0.002 TYR A 435 ARG 0.005 0.001 ARG A 190 *********************** 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 : 0.426 Fit side-chains REVERT: A 300 LYS cc_start: 0.8549 (mttt) cc_final: 0.7984 (tttm) REVERT: A 361 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8340 (tptp) REVERT: A 503 ARG cc_start: 0.8368 (mtm180) cc_final: 0.7986 (ptm160) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1171 time to fit residues: 15.3223 Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1528 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= 0.214 Angle : 0.634 6.866 5083 Z= 0.329 Chirality : 0.045 0.166 598 Planarity : 0.006 0.055 627 Dihedral : 4.949 23.931 501 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.07 % Allowed : 13.67 % Favored : 85.25 % 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: -1.11 (0.40), residues: 471 helix: 0.30 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -3.00 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.025 0.002 PHE A 134 TYR 0.016 0.001 TYR A 55 ARG 0.003 0.000 ARG A 190 *********************** 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 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.8183 (tp) cc_final: 0.7948 (tp) REVERT: A 137 ASP cc_start: 0.7453 (t0) cc_final: 0.7072 (t0) REVERT: A 300 LYS cc_start: 0.8555 (mttt) cc_final: 0.7943 (tttm) REVERT: A 361 LYS cc_start: 0.8521 (tmtt) cc_final: 0.7970 (tptp) REVERT: A 381 MET cc_start: 0.5126 (ttt) cc_final: 0.4678 (ttm) REVERT: A 409 MET cc_start: 0.7800 (ttt) cc_final: 0.7491 (mtp) REVERT: A 503 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7908 (ptm160) outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.1129 time to fit residues: 13.5537 Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 299 VAL 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: 0.6980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3725 Z= 0.221 Angle : 0.607 6.756 5083 Z= 0.315 Chirality : 0.045 0.187 598 Planarity : 0.005 0.050 627 Dihedral : 4.748 22.512 501 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.14 % Allowed : 18.77 % Favored : 79.09 % 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: -0.91 (0.40), residues: 471 helix: 0.46 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.98 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.001 0.000 HIS A 67 PHE 0.032 0.002 PHE A 134 TYR 0.008 0.001 TYR A 55 ARG 0.003 0.000 ARG A 190 *********************** 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 98 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7458 (t0) cc_final: 0.6994 (t0) REVERT: A 300 LYS cc_start: 0.8531 (mttt) cc_final: 0.7954 (tttm) REVERT: A 334 GLN cc_start: 0.8060 (pt0) cc_final: 0.7629 (mt0) REVERT: A 361 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8032 (tptp) REVERT: A 381 MET cc_start: 0.5039 (ttt) cc_final: 0.4618 (ttm) REVERT: A 409 MET cc_start: 0.7967 (ttt) cc_final: 0.7739 (mtp) REVERT: A 503 ARG cc_start: 0.8422 (mtm180) cc_final: 0.8181 (mtm180) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1292 time to fit residues: 15.2932 Evaluate side-chains 87 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3725 Z= 0.215 Angle : 0.617 8.506 5083 Z= 0.313 Chirality : 0.044 0.166 598 Planarity : 0.005 0.047 627 Dihedral : 4.642 22.703 501 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.56 % Allowed : 20.11 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.41), residues: 471 helix: 0.65 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.86 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.001 0.000 HIS A 67 PHE 0.032 0.002 PHE A 134 TYR 0.017 0.001 TYR A 55 ARG 0.003 0.000 ARG A 504 *********************** 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 104 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7303 (t0) cc_final: 0.6798 (t0) REVERT: A 164 CYS cc_start: 0.9328 (t) cc_final: 0.9081 (t) REVERT: A 300 LYS cc_start: 0.8519 (mttt) cc_final: 0.7950 (tttm) REVERT: A 334 GLN cc_start: 0.8091 (pt0) cc_final: 0.7626 (mt0) REVERT: A 361 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8057 (tptp) REVERT: A 381 MET cc_start: 0.5031 (ttt) cc_final: 0.4553 (ttm) REVERT: A 409 MET cc_start: 0.7984 (ttt) cc_final: 0.7775 (mtp) REVERT: A 503 ARG cc_start: 0.8394 (mtm180) cc_final: 0.7965 (ptm160) REVERT: A 508 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8351 (mmtm) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.1107 time to fit residues: 13.7407 Evaluate side-chains 91 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.2453 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= 0.174 Angle : 0.596 8.597 5083 Z= 0.300 Chirality : 0.044 0.208 598 Planarity : 0.005 0.046 627 Dihedral : 4.456 21.974 501 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.75 % Allowed : 21.98 % Favored : 74.26 % 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: -0.46 (0.41), residues: 471 helix: 0.78 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.76 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS A 166 PHE 0.033 0.002 PHE A 134 TYR 0.012 0.001 TYR A 435 ARG 0.002 0.000 ARG A 504 *********************** 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 111 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7108 (t0) cc_final: 0.6583 (t0) REVERT: A 164 CYS cc_start: 0.9332 (t) cc_final: 0.9115 (t) REVERT: A 300 LYS cc_start: 0.8490 (mttt) cc_final: 0.7928 (tttm) REVERT: A 334 GLN cc_start: 0.8005 (pt0) cc_final: 0.7579 (mt0) REVERT: A 361 LYS cc_start: 0.8628 (tmtt) cc_final: 0.8067 (tptp) REVERT: A 381 MET cc_start: 0.4840 (ttt) cc_final: 0.4320 (ttm) REVERT: A 409 MET cc_start: 0.7964 (ttt) cc_final: 0.7751 (mtp) REVERT: A 503 ARG cc_start: 0.8427 (mtm180) cc_final: 0.7992 (ptm160) REVERT: A 508 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8358 (mmtm) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 0.1114 time to fit residues: 15.3555 Evaluate side-chains 91 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3725 Z= 0.184 Angle : 0.594 8.138 5083 Z= 0.297 Chirality : 0.044 0.203 598 Planarity : 0.005 0.044 627 Dihedral : 4.403 22.466 501 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.49 % Allowed : 23.59 % Favored : 72.92 % 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: 0.90 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.75 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.032 0.001 PHE A 134 TYR 0.018 0.001 TYR A 55 ARG 0.002 0.000 ARG A 504 *********************** 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 106 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7118 (t0) cc_final: 0.6586 (t0) REVERT: A 164 CYS cc_start: 0.9324 (t) cc_final: 0.9118 (t) REVERT: A 300 LYS cc_start: 0.8534 (mttt) cc_final: 0.7922 (tttm) REVERT: A 334 GLN cc_start: 0.8013 (pt0) cc_final: 0.7573 (mt0) REVERT: A 361 LYS cc_start: 0.8615 (tmtt) cc_final: 0.7977 (tptp) REVERT: A 381 MET cc_start: 0.4890 (ttt) cc_final: 0.4367 (ttm) REVERT: A 409 MET cc_start: 0.8017 (ttt) cc_final: 0.7771 (mtp) REVERT: A 503 ARG cc_start: 0.8446 (mtm180) cc_final: 0.8007 (ptm160) REVERT: A 508 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8348 (mmtm) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.1058 time to fit residues: 14.0458 Evaluate side-chains 100 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 486 ILE 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: 9.9990 chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 0.0030 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3725 Z= 0.163 Angle : 0.578 8.283 5083 Z= 0.288 Chirality : 0.043 0.197 598 Planarity : 0.005 0.043 627 Dihedral : 4.306 21.712 501 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.68 % Allowed : 26.01 % Favored : 71.31 % 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: -0.26 (0.41), residues: 471 helix: 0.95 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.81 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.001 0.000 HIS A 146 PHE 0.031 0.001 PHE A 134 TYR 0.009 0.001 TYR A 55 ARG 0.001 0.000 ARG A 190 *********************** 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 108 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7041 (t0) cc_final: 0.6517 (t0) REVERT: A 300 LYS cc_start: 0.8553 (mttt) cc_final: 0.7881 (tttm) REVERT: A 334 GLN cc_start: 0.7956 (pt0) cc_final: 0.7516 (mt0) REVERT: A 361 LYS cc_start: 0.8580 (tmtt) cc_final: 0.7983 (tptp) REVERT: A 381 MET cc_start: 0.4784 (ttt) cc_final: 0.4227 (ttm) REVERT: A 409 MET cc_start: 0.8022 (ttt) cc_final: 0.7798 (mtp) REVERT: A 499 ASP cc_start: 0.7353 (t0) cc_final: 0.7128 (t70) REVERT: A 503 ARG cc_start: 0.8471 (mtm180) cc_final: 0.7968 (ptm160) REVERT: A 508 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8423 (mmtm) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1046 time to fit residues: 14.3013 Evaluate side-chains 99 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3725 Z= 0.170 Angle : 0.577 7.547 5083 Z= 0.288 Chirality : 0.043 0.199 598 Planarity : 0.005 0.042 627 Dihedral : 4.277 22.385 501 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.41 % Allowed : 28.42 % Favored : 69.17 % 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: -0.04 (0.41), residues: 471 helix: 1.12 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.69 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.002 0.000 HIS A 166 PHE 0.032 0.001 PHE A 134 TYR 0.018 0.001 TYR A 55 ARG 0.001 0.000 ARG A 190 *********************** 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 104 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7088 (t0) cc_final: 0.6545 (t0) REVERT: A 300 LYS cc_start: 0.8570 (mttt) cc_final: 0.7892 (tttm) REVERT: A 334 GLN cc_start: 0.7972 (pt0) cc_final: 0.7561 (mt0) REVERT: A 361 LYS cc_start: 0.8593 (tmtt) cc_final: 0.8007 (tptp) REVERT: A 381 MET cc_start: 0.4793 (ttt) cc_final: 0.4233 (ttm) REVERT: A 409 MET cc_start: 0.8085 (ttt) cc_final: 0.7861 (mtp) REVERT: A 458 ASN cc_start: 0.6997 (m110) cc_final: 0.6781 (m110) REVERT: A 503 ARG cc_start: 0.8459 (mtm180) cc_final: 0.8216 (mtm180) REVERT: A 508 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8441 (mmtm) outliers start: 9 outliers final: 9 residues processed: 102 average time/residue: 0.1079 time to fit residues: 14.6718 Evaluate side-chains 100 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3725 Z= 0.165 Angle : 0.590 7.742 5083 Z= 0.291 Chirality : 0.043 0.196 598 Planarity : 0.005 0.042 627 Dihedral : 4.279 22.210 501 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.68 % Allowed : 28.42 % Favored : 68.90 % 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: 0.03 (0.42), residues: 471 helix: 1.11 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.67 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.001 0.000 HIS A 166 PHE 0.031 0.002 PHE A 134 TYR 0.017 0.001 TYR A 55 ARG 0.002 0.000 ARG A 190 *********************** 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 101 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 109 THR cc_start: 0.9531 (t) cc_final: 0.9268 (p) REVERT: A 137 ASP cc_start: 0.7071 (t0) cc_final: 0.6534 (t0) REVERT: A 300 LYS cc_start: 0.8581 (mttt) cc_final: 0.7898 (tttm) REVERT: A 334 GLN cc_start: 0.7931 (pt0) cc_final: 0.7526 (mt0) REVERT: A 361 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8000 (tptp) REVERT: A 381 MET cc_start: 0.4745 (ttt) cc_final: 0.4203 (ttm) REVERT: A 409 MET cc_start: 0.8094 (ttt) cc_final: 0.7860 (mtp) REVERT: A 458 ASN cc_start: 0.6990 (m110) cc_final: 0.6780 (m110) REVERT: A 503 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7926 (ptm160) REVERT: A 508 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8457 (mmtm) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.1079 time to fit residues: 14.0731 Evaluate side-chains 95 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3725 Z= 0.170 Angle : 0.584 8.158 5083 Z= 0.289 Chirality : 0.043 0.192 598 Planarity : 0.005 0.041 627 Dihedral : 4.270 22.042 501 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.14 % Allowed : 29.49 % Favored : 68.36 % 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: 0.15 (0.41), residues: 471 helix: 1.23 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.71 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.002 0.000 HIS A 166 PHE 0.030 0.001 PHE A 134 TYR 0.018 0.001 TYR A 55 ARG 0.001 0.000 ARG A 190 ********************** 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 97 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 109 THR cc_start: 0.9513 (t) cc_final: 0.9230 (p) REVERT: A 137 ASP cc_start: 0.7058 (t0) cc_final: 0.6544 (t0) REVERT: A 300 LYS cc_start: 0.8570 (mttt) cc_final: 0.7873 (tttm) REVERT: A 334 GLN cc_start: 0.7957 (pt0) cc_final: 0.7553 (mt0) REVERT: A 361 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8016 (tptp) REVERT: A 381 MET cc_start: 0.4731 (ttt) cc_final: 0.4179 (ttm) REVERT: A 409 MET cc_start: 0.8147 (ttt) cc_final: 0.7914 (mtp) REVERT: A 503 ARG cc_start: 0.8388 (mtm180) cc_final: 0.7950 (ptm160) REVERT: A 508 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8472 (mmtm) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.1113 time to fit residues: 14.2726 Evaluate side-chains 94 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102698 restraints weight = 6952.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106261 restraints weight = 3647.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108878 restraints weight = 2366.074| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3725 Z= 0.172 Angle : 0.606 11.290 5083 Z= 0.297 Chirality : 0.043 0.189 598 Planarity : 0.005 0.041 627 Dihedral : 4.269 22.148 501 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.14 % Allowed : 29.76 % Favored : 68.10 % 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: 1.24 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.70 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.002 0.000 HIS A 166 PHE 0.032 0.001 PHE A 134 TYR 0.018 0.001 TYR A 55 ARG 0.001 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.10 seconds wall clock time: 20 minutes 39.81 seconds (1239.81 seconds total)