Starting phenix.real_space_refine on Fri Apr 5 15:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc3_40336/04_2024/8sc3_40336_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 30 5.16 5 C 2284 2.51 5 N 559 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3463 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3441 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'ZVJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.65 Number of scatterers: 3463 At special positions: 0 Unit cell: (89.64, 83, 63.91, 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 30 16.00 O 590 8.00 N 559 7.00 C 2284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " 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: 1.34 Conformation dependent library (CDL) restraints added in 818.5 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 1 sheets defined 74.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 Proline residue: A 34 - end of helix removed outlier: 5.240A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.681A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 163 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.600A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 4.241A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 Processing helix chain 'A' and resid 261 through 277 Proline residue: A 271 - end of helix removed outlier: 3.560A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 341 through 371 Processing helix chain 'A' and resid 375 through 399 removed outlier: 3.579A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 4.101A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.862A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 4.116A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 489 removed outlier: 4.432A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 4.333A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.652A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 228 hydrogen bonds defined for protein. 603 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: 0.92 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1063 1.35 - 1.47: 914 1.47 - 1.59: 1531 1.59 - 1.71: 1 1.71 - 1.83: 45 Bond restraints: 3554 Sorted by residual: bond pdb=" C01 ZVJ A 601 " pdb=" C02 ZVJ A 601 " ideal model delta sigma weight residual 1.496 1.565 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C11 ZVJ A 601 " pdb=" C13 ZVJ A 601 " ideal model delta sigma weight residual 1.367 1.434 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C19 ZVJ A 601 " pdb=" C20 ZVJ A 601 " ideal model delta sigma weight residual 1.379 1.445 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C08 ZVJ A 601 " pdb=" O09 ZVJ A 601 " ideal model delta sigma weight residual 1.389 1.451 -0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" C20 ZVJ A 601 " pdb=" C21 ZVJ A 601 " ideal model delta sigma weight residual 1.400 1.343 0.057 2.00e-02 2.50e+03 8.24e+00 ... (remaining 3549 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 119 106.87 - 113.64: 1923 113.64 - 120.41: 1396 120.41 - 127.18: 1358 127.18 - 133.95: 47 Bond angle restraints: 4843 Sorted by residual: angle pdb=" C10 ZVJ A 601 " pdb=" C11 ZVJ A 601 " pdb=" O12 ZVJ A 601 " ideal model delta sigma weight residual 106.44 120.01 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C13 ZVJ A 601 " pdb=" C11 ZVJ A 601 " pdb=" O12 ZVJ A 601 " ideal model delta sigma weight residual 132.45 120.05 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C18 ZVJ A 601 " pdb=" C19 ZVJ A 601 " pdb=" O22 ZVJ A 601 " ideal model delta sigma weight residual 111.24 120.03 -8.79 3.00e+00 1.11e-01 8.59e+00 angle pdb=" C20 ZVJ A 601 " pdb=" C19 ZVJ A 601 " pdb=" O22 ZVJ A 601 " ideal model delta sigma weight residual 128.67 119.94 8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" C05 ZVJ A 601 " pdb=" C04 ZVJ A 601 " pdb=" N03 ZVJ A 601 " ideal model delta sigma weight residual 109.49 118.14 -8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 4838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 1939 16.82 - 33.63: 92 33.63 - 50.44: 24 50.44 - 67.26: 3 67.26 - 84.07: 2 Dihedral angle restraints: 2060 sinusoidal: 787 harmonic: 1273 Sorted by residual: dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " pdb=" CD GLU A 515 " pdb=" OE1 GLU A 515 " ideal model delta sinusoidal sigma weight residual 0.00 -84.07 84.07 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU A 489 " pdb=" CG GLU A 489 " pdb=" CD GLU A 489 " pdb=" OE1 GLU A 489 " ideal model delta sinusoidal sigma weight residual 0.00 81.08 -81.08 1 3.00e+01 1.11e-03 9.01e+00 ... (remaining 2057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 424 0.041 - 0.082: 113 0.082 - 0.123: 23 0.123 - 0.164: 1 0.164 - 0.205: 1 Chirality restraints: 562 Sorted by residual: chirality pdb=" C05 ZVJ A 601 " pdb=" C04 ZVJ A 601 " pdb=" C06 ZVJ A 601 " pdb=" O14 ZVJ A 601 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 559 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C MET A 406 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 28 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU A 28 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 28 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 239 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C MET A 239 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 239 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 240 " 0.013 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 301 2.74 - 3.28: 3778 3.28 - 3.82: 5826 3.82 - 4.36: 6809 4.36 - 4.90: 11726 Nonbonded interactions: 28440 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.206 2.440 nonbonded pdb=" NH1 ARG A 90 " pdb=" OD2 ASP A 123 " model vdw 2.407 2.520 nonbonded pdb=" O ALA A 194 " pdb=" NH1 ARG A 262 " model vdw 2.409 2.520 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.469 2.440 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 216 " model vdw 2.488 2.440 ... (remaining 28435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 3.600 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 0.069 3554 Z= 0.284 Angle : 0.709 13.567 4843 Z= 0.385 Chirality : 0.038 0.205 562 Planarity : 0.006 0.037 597 Dihedral : 11.479 84.073 1237 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.54 (0.38), residues: 441 helix: -0.50 (0.26), residues: 317 sheet: None (None), residues: 0 loop : 0.60 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 261 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.002 PHE A 151 TYR 0.021 0.002 TYR A 72 ARG 0.008 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8137 (m-30) cc_final: 0.7845 (m-30) REVERT: A 116 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (mp) REVERT: A 150 LEU cc_start: 0.8883 (tp) cc_final: 0.8647 (tt) REVERT: A 154 CYS cc_start: 0.8293 (m) cc_final: 0.8035 (m) REVERT: A 392 ILE cc_start: 0.8580 (mt) cc_final: 0.8255 (mt) REVERT: A 460 PHE cc_start: 0.4975 (t80) cc_final: 0.4646 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1490 time to fit residues: 24.6954 Evaluate side-chains 106 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3554 Z= 0.216 Angle : 0.598 5.816 4843 Z= 0.307 Chirality : 0.038 0.129 562 Planarity : 0.005 0.041 597 Dihedral : 5.749 56.525 485 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 4.88 % Allowed : 7.05 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.42), residues: 441 helix: 1.38 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 1.70 (0.70), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.020 0.002 PHE A 227 TYR 0.021 0.002 TYR A 240 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8070 (m-30) cc_final: 0.7757 (m-30) REVERT: A 68 GLU cc_start: 0.7879 (tt0) cc_final: 0.7624 (tm-30) REVERT: A 116 LEU cc_start: 0.8595 (mt) cc_final: 0.8259 (mp) REVERT: A 239 MET cc_start: 0.7278 (tpt) cc_final: 0.6811 (tpt) REVERT: A 410 ASN cc_start: 0.8315 (m-40) cc_final: 0.8078 (m110) REVERT: A 429 TRP cc_start: 0.7105 (p-90) cc_final: 0.6892 (p90) outliers start: 18 outliers final: 10 residues processed: 130 average time/residue: 0.1321 time to fit residues: 21.5632 Evaluate side-chains 106 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3554 Z= 0.188 Angle : 0.585 8.441 4843 Z= 0.298 Chirality : 0.038 0.165 562 Planarity : 0.004 0.045 597 Dihedral : 5.322 41.282 485 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 5.96 % Allowed : 11.11 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.42), residues: 441 helix: 1.76 (0.30), residues: 319 sheet: None (None), residues: 0 loop : 1.45 (0.67), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 PHE 0.011 0.001 PHE A 348 TYR 0.017 0.001 TYR A 361 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8072 (m-30) cc_final: 0.7775 (m-30) REVERT: A 242 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7067 (ppp) REVERT: A 351 MET cc_start: 0.6992 (mtt) cc_final: 0.6590 (tmm) REVERT: A 410 ASN cc_start: 0.8204 (m-40) cc_final: 0.8002 (m-40) REVERT: A 457 TYR cc_start: 0.7395 (m-80) cc_final: 0.7000 (m-80) outliers start: 22 outliers final: 14 residues processed: 113 average time/residue: 0.1171 time to fit residues: 17.0820 Evaluate side-chains 109 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3554 Z= 0.212 Angle : 0.588 7.755 4843 Z= 0.299 Chirality : 0.039 0.175 562 Planarity : 0.004 0.044 597 Dihedral : 5.397 39.404 485 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 5.96 % Allowed : 13.01 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.42), residues: 441 helix: 1.66 (0.29), residues: 326 sheet: None (None), residues: 0 loop : 1.48 (0.69), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.002 PHE A 348 TYR 0.017 0.002 TYR A 240 ARG 0.006 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8061 (m-30) cc_final: 0.7790 (m-30) REVERT: A 239 MET cc_start: 0.7267 (tpt) cc_final: 0.6857 (tpt) REVERT: A 334 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7339 (m-80) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.1088 time to fit residues: 15.1119 Evaluate side-chains 109 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3554 Z= 0.160 Angle : 0.559 6.984 4843 Z= 0.283 Chirality : 0.038 0.227 562 Planarity : 0.004 0.044 597 Dihedral : 5.337 42.599 485 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 6.50 % Allowed : 13.82 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.43), residues: 441 helix: 1.83 (0.30), residues: 324 sheet: None (None), residues: 0 loop : 1.56 (0.69), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.014 0.001 PHE A 348 TYR 0.016 0.001 TYR A 361 ARG 0.007 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8079 (m-30) cc_final: 0.7801 (m-30) REVERT: A 69 GLU cc_start: 0.8800 (tt0) cc_final: 0.8579 (pp20) REVERT: A 239 MET cc_start: 0.7188 (tpt) cc_final: 0.6783 (tpt) REVERT: A 435 MET cc_start: 0.8091 (ttp) cc_final: 0.7629 (mtt) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.1293 time to fit residues: 17.3880 Evaluate side-chains 103 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.7857 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3554 Z= 0.182 Angle : 0.560 5.945 4843 Z= 0.287 Chirality : 0.039 0.223 562 Planarity : 0.004 0.042 597 Dihedral : 5.363 43.356 485 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.96 % Allowed : 15.18 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.43), residues: 441 helix: 1.77 (0.30), residues: 325 sheet: None (None), residues: 0 loop : 1.41 (0.69), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.019 0.001 PHE A 391 TYR 0.018 0.001 TYR A 361 ARG 0.008 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.442 Fit side-chains REVERT: A 47 ASP cc_start: 0.8063 (m-30) cc_final: 0.7783 (m-30) REVERT: A 69 GLU cc_start: 0.8818 (tt0) cc_final: 0.8574 (pp20) REVERT: A 239 MET cc_start: 0.7221 (tpt) cc_final: 0.6888 (tpt) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.1151 time to fit residues: 14.6392 Evaluate side-chains 97 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3554 Z= 0.189 Angle : 0.567 5.920 4843 Z= 0.291 Chirality : 0.040 0.226 562 Planarity : 0.005 0.042 597 Dihedral : 5.463 40.668 485 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 7.05 % Allowed : 14.36 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.42), residues: 441 helix: 1.72 (0.30), residues: 325 sheet: None (None), residues: 0 loop : 1.35 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.012 0.001 PHE A 244 TYR 0.017 0.001 TYR A 361 ARG 0.009 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8059 (m-30) cc_final: 0.7779 (m-30) REVERT: A 69 GLU cc_start: 0.8824 (tt0) cc_final: 0.8567 (pp20) REVERT: A 233 ARG cc_start: 0.7412 (ptp-170) cc_final: 0.7175 (ptp-170) REVERT: A 239 MET cc_start: 0.7239 (tpt) cc_final: 0.6920 (tpt) outliers start: 26 outliers final: 18 residues processed: 98 average time/residue: 0.1096 time to fit residues: 14.1617 Evaluate side-chains 98 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3554 Z= 0.229 Angle : 0.602 5.964 4843 Z= 0.308 Chirality : 0.041 0.223 562 Planarity : 0.005 0.042 597 Dihedral : 5.507 41.338 485 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.96 % Allowed : 15.72 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.42), residues: 441 helix: 1.63 (0.29), residues: 325 sheet: None (None), residues: 0 loop : 1.26 (0.67), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.024 0.002 PHE A 391 TYR 0.019 0.001 TYR A 361 ARG 0.010 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.377 Fit side-chains REVERT: A 69 GLU cc_start: 0.8795 (tt0) cc_final: 0.8549 (pp20) REVERT: A 233 ARG cc_start: 0.7444 (ptp-170) cc_final: 0.7239 (ptp-170) REVERT: A 239 MET cc_start: 0.7231 (tpt) cc_final: 0.6938 (tpt) outliers start: 22 outliers final: 20 residues processed: 90 average time/residue: 0.1161 time to fit residues: 13.6385 Evaluate side-chains 100 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3554 Z= 0.177 Angle : 0.571 5.645 4843 Z= 0.294 Chirality : 0.040 0.229 562 Planarity : 0.005 0.043 597 Dihedral : 5.441 40.723 485 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.15 % Allowed : 17.34 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.42), residues: 441 helix: 1.66 (0.30), residues: 325 sheet: None (None), residues: 0 loop : 1.26 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.014 0.001 PHE A 348 TYR 0.017 0.001 TYR A 361 ARG 0.011 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.338 Fit side-chains REVERT: A 47 ASP cc_start: 0.8072 (m-30) cc_final: 0.7789 (m-30) REVERT: A 239 MET cc_start: 0.7206 (tpt) cc_final: 0.6986 (tpt) REVERT: A 447 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7436 (tp40) outliers start: 19 outliers final: 14 residues processed: 92 average time/residue: 0.1152 time to fit residues: 13.7991 Evaluate side-chains 93 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.0030 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 35 optimal weight: 0.5980 overall best weight: 0.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3554 Z= 0.145 Angle : 0.574 5.962 4843 Z= 0.293 Chirality : 0.039 0.233 562 Planarity : 0.005 0.050 597 Dihedral : 5.294 39.171 485 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.71 % Allowed : 20.33 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.43), residues: 441 helix: 1.75 (0.30), residues: 326 sheet: None (None), residues: 0 loop : 1.24 (0.68), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.001 0.000 HIS A 49 PHE 0.025 0.001 PHE A 391 TYR 0.015 0.001 TYR A 361 ARG 0.012 0.001 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.440 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.1070 time to fit residues: 12.2100 Evaluate side-chains 86 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 0.0570 chunk 30 optimal weight: 0.0470 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.203712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165156 restraints weight = 4759.103| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.93 r_work: 0.3715 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3554 Z= 0.167 Angle : 0.655 12.993 4843 Z= 0.319 Chirality : 0.043 0.285 562 Planarity : 0.005 0.048 597 Dihedral : 5.271 39.845 485 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 21.41 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.43), residues: 441 helix: 1.69 (0.30), residues: 325 sheet: None (None), residues: 0 loop : 1.18 (0.68), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.001 0.000 HIS A 49 PHE 0.018 0.001 PHE A 348 TYR 0.018 0.001 TYR A 361 ARG 0.012 0.001 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.04 seconds wall clock time: 23 minutes 17.32 seconds (1397.32 seconds total)