Starting phenix.real_space_refine on Mon Sep 23 16:53:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1m_44084/09_2024/9b1m_44084.cif" } resolution = 3.0 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 2582 2.51 5 N 667 2.21 5 O 682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3961 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3938 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Conformer: "B" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} bond proxies already assigned to first conformer: 4002 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1, 'VGL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.81, per 1000 atoms: 1.47 Number of scatterers: 3961 At special positions: 0 Unit cell: (55.814, 87.615, 102.542, 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 682 8.00 N 667 7.00 C 2582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 81.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.849A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.625A pdb=" N SER A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.821A pdb=" N ALA A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.664A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.793A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) 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 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.691A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.591A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.540A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.152A pdb=" N APHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.101A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.528A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 4.057A pdb=" N LYS A 309 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.789A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 333 through 339 removed outlier: 4.058A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.659A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.761A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.632A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.672A pdb=" N ILE A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.652A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.632A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.151A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.629A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 260 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.24 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: 1249 1.35 - 1.47: 967 1.47 - 1.58: 1800 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4063 Sorted by residual: bond pdb=" N PHE A 3 " pdb=" CA PHE A 3 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.27e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.51e+00 bond pdb=" C MET A 211 " pdb=" O MET A 211 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.43e+00 bond pdb=" C VAL A 26 " pdb=" O VAL A 26 " ideal model delta sigma weight residual 1.237 1.251 -0.014 1.17e-02 7.31e+03 1.41e+00 ... (remaining 4058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 5241 1.47 - 2.94: 241 2.94 - 4.40: 48 4.40 - 5.87: 13 5.87 - 7.34: 2 Bond angle restraints: 5545 Sorted by residual: angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 121.24 -7.34 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C LEU A 271 " pdb=" N TYR A 272 " pdb=" CA TYR A 272 " ideal model delta sigma weight residual 121.58 116.20 5.38 1.95e+00 2.63e-01 7.60e+00 angle pdb=" C VAL A 264 " pdb=" CA VAL A 264 " pdb=" CB VAL A 264 " ideal model delta sigma weight residual 114.35 111.52 2.83 1.06e+00 8.90e-01 7.14e+00 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 118.62 -4.72 1.80e+00 3.09e-01 6.87e+00 angle pdb=" C VAL A 230 " pdb=" N MET A 231 " pdb=" CA MET A 231 " ideal model delta sigma weight residual 120.31 116.37 3.94 1.52e+00 4.33e-01 6.71e+00 ... (remaining 5540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2261 16.82 - 33.63: 110 33.63 - 50.45: 26 50.45 - 67.26: 4 67.26 - 84.08: 4 Dihedral angle restraints: 2405 sinusoidal: 925 harmonic: 1480 Sorted by residual: dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta harmonic sigma weight residual 180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 417 0.034 - 0.067: 163 0.067 - 0.101: 52 0.101 - 0.134: 17 0.134 - 0.168: 4 Chirality restraints: 653 Sorted by residual: chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CB ILE A 153 " pdb=" CA ILE A 153 " pdb=" CG1 ILE A 153 " pdb=" CG2 ILE A 153 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 650 not shown) Planarity restraints: 693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " -0.020 2.00e-02 2.50e+03 1.37e-02 3.77e+00 pdb=" CG TYR A 272 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 265 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 480 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.022 5.00e-02 4.00e+02 ... (remaining 690 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1718 2.92 - 3.42: 4066 3.42 - 3.91: 6448 3.91 - 4.41: 7711 4.41 - 4.90: 12208 Nonbonded interactions: 32151 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.431 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.477 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.510 3.040 nonbonded pdb=" N ASP A 290 " pdb=" OD1 ASP A 290 " model vdw 2.528 3.120 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.540 3.040 ... (remaining 32146 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=0.31 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: 2.630 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.037 4063 Z= 0.279 Angle : 0.765 7.338 5545 Z= 0.421 Chirality : 0.043 0.168 653 Planarity : 0.006 0.055 692 Dihedral : 11.395 84.081 1445 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.34), residues: 517 helix: -0.24 (0.24), residues: 377 sheet: None (None), residues: 0 loop : 1.24 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.002 0.001 HIS A 424 PHE 0.022 0.002 PHE A 344 TYR 0.033 0.002 TYR A 272 ARG 0.003 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.422 Fit side-chains REVERT: A 219 MET cc_start: 0.6324 (mmp) cc_final: 0.6091 (mmp) REVERT: A 281 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7208 (mtm-85) REVERT: A 488 HIS cc_start: 0.7581 (m170) cc_final: 0.7346 (m170) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.0953 time to fit residues: 80.6453 Evaluate side-chains 46 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 368 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4063 Z= 0.200 Angle : 0.613 8.611 5545 Z= 0.305 Chirality : 0.040 0.131 653 Planarity : 0.005 0.042 692 Dihedral : 4.653 49.646 574 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.67 % Allowed : 9.33 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.36), residues: 517 helix: 0.90 (0.26), residues: 370 sheet: None (None), residues: 0 loop : 1.76 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.002 PHE A 356 TYR 0.021 0.002 TYR A 272 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.418 Fit side-chains REVERT: A 95 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 281 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7056 (mtm-85) REVERT: A 459 VAL cc_start: 0.8179 (m) cc_final: 0.7907 (p) REVERT: A 462 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.3942 (mpt) REVERT: A 497 TYR cc_start: 0.8540 (m-80) cc_final: 0.8335 (m-80) outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 0.9661 time to fit residues: 46.5007 Evaluate side-chains 47 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 488 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4063 Z= 0.209 Angle : 0.592 8.218 5545 Z= 0.287 Chirality : 0.039 0.136 653 Planarity : 0.005 0.038 692 Dihedral : 4.173 40.171 574 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.63 % Allowed : 9.33 % Favored : 88.04 % 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: 1.70 (0.37), residues: 517 helix: 1.13 (0.27), residues: 371 sheet: -1.27 (1.45), residues: 10 loop : 1.76 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 242 PHE 0.013 0.002 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.006 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.314 Fit side-chains REVERT: A 126 SER cc_start: 0.8626 (t) cc_final: 0.8066 (m) REVERT: A 219 MET cc_start: 0.5855 (mmp) cc_final: 0.4875 (mtt) REVERT: A 281 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.7250 (mtm-85) REVERT: A 297 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6754 (mtt-85) REVERT: A 462 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4081 (mpt) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 0.7412 time to fit residues: 41.3354 Evaluate side-chains 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 0.035 4063 Z= 0.187 Angle : 0.557 7.162 5545 Z= 0.269 Chirality : 0.039 0.143 653 Planarity : 0.005 0.037 692 Dihedral : 3.870 33.665 574 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.63 % Allowed : 9.57 % Favored : 87.80 % 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 (0.37), residues: 517 helix: 1.56 (0.27), residues: 359 sheet: -1.81 (1.46), residues: 10 loop : 1.42 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.011 0.001 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.007 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.430 Fit side-chains REVERT: A 126 SER cc_start: 0.8595 (t) cc_final: 0.8014 (m) REVERT: A 219 MET cc_start: 0.5734 (mmp) cc_final: 0.4770 (mtt) REVERT: A 281 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7200 (mtm-85) REVERT: A 462 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4051 (mpt) outliers start: 11 outliers final: 3 residues processed: 49 average time/residue: 0.8907 time to fit residues: 45.8787 Evaluate side-chains 47 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4063 Z= 0.209 Angle : 0.567 7.600 5545 Z= 0.274 Chirality : 0.039 0.140 653 Planarity : 0.004 0.036 692 Dihedral : 3.827 31.999 574 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.91 % Allowed : 10.53 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.37), residues: 517 helix: 1.59 (0.27), residues: 358 sheet: -1.80 (1.59), residues: 10 loop : 1.42 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.435 Fit side-chains REVERT: A 126 SER cc_start: 0.8573 (t) cc_final: 0.7984 (m) REVERT: A 281 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7201 (mtm-85) REVERT: A 297 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6841 (mtt-85) REVERT: A 462 MET cc_start: 0.4718 (OUTLIER) cc_final: 0.4088 (mpt) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 1.0897 time to fit residues: 52.3257 Evaluate side-chains 47 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4063 Z= 0.194 Angle : 0.555 8.525 5545 Z= 0.267 Chirality : 0.038 0.139 653 Planarity : 0.004 0.035 692 Dihedral : 3.728 29.669 574 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.20 % Allowed : 12.20 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.37), residues: 517 helix: 1.68 (0.27), residues: 358 sheet: -1.91 (1.62), residues: 10 loop : 1.47 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.021 0.002 TYR A 272 ARG 0.006 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.445 Fit side-chains REVERT: A 126 SER cc_start: 0.8557 (t) cc_final: 0.7950 (m) REVERT: A 281 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7180 (mtm-85) REVERT: A 462 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4132 (mpt) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.9261 time to fit residues: 43.8619 Evaluate side-chains 48 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.0270 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 419 ASN A 488 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4063 Z= 0.174 Angle : 0.540 7.686 5545 Z= 0.261 Chirality : 0.038 0.139 653 Planarity : 0.004 0.034 692 Dihedral : 3.673 28.512 574 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.39 % Allowed : 11.00 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.37), residues: 517 helix: 1.78 (0.27), residues: 359 sheet: -1.98 (1.65), residues: 10 loop : 1.48 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 305 PHE 0.012 0.001 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.394 Fit side-chains REVERT: A 126 SER cc_start: 0.8541 (t) cc_final: 0.7930 (m) REVERT: A 281 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7161 (mtm-85) REVERT: A 297 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6918 (mtt-85) REVERT: A 462 MET cc_start: 0.4772 (OUTLIER) cc_final: 0.4157 (mpt) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.9343 time to fit residues: 46.9557 Evaluate side-chains 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4063 Z= 0.205 Angle : 0.564 8.891 5545 Z= 0.270 Chirality : 0.039 0.140 653 Planarity : 0.004 0.034 692 Dihedral : 3.670 27.448 574 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.15 % Allowed : 11.24 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.37), residues: 517 helix: 1.75 (0.27), residues: 358 sheet: -1.72 (1.78), residues: 10 loop : 1.49 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 358 TYR 0.021 0.002 TYR A 272 ARG 0.007 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.463 Fit side-chains REVERT: A 90 GLN cc_start: 0.8023 (mm110) cc_final: 0.7764 (mp10) REVERT: A 120 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7696 (t0) REVERT: A 126 SER cc_start: 0.8561 (t) cc_final: 0.7953 (m) REVERT: A 281 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.7166 (mtm-85) REVERT: A 297 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6996 (mtt-85) REVERT: A 462 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.4219 (mpt) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 1.1955 time to fit residues: 62.0841 Evaluate side-chains 56 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4063 Z= 0.251 Angle : 0.594 8.262 5545 Z= 0.287 Chirality : 0.040 0.139 653 Planarity : 0.004 0.035 692 Dihedral : 3.680 27.773 574 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.63 % Allowed : 10.53 % Favored : 86.84 % 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: 2.17 (0.37), residues: 517 helix: 1.68 (0.27), residues: 357 sheet: -1.63 (1.88), residues: 10 loop : 1.35 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.007 0.001 HIS A 305 PHE 0.014 0.002 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.006 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.448 Fit side-chains REVERT: A 5 GLU cc_start: 0.6647 (pm20) cc_final: 0.6426 (pm20) REVERT: A 38 GLU cc_start: 0.8569 (tt0) cc_final: 0.8081 (tp30) REVERT: A 90 GLN cc_start: 0.8024 (mm110) cc_final: 0.7783 (mp10) REVERT: A 120 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7720 (t0) REVERT: A 126 SER cc_start: 0.8555 (t) cc_final: 0.7953 (m) REVERT: A 281 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7164 (mtm-85) REVERT: A 297 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7002 (mtt-85) REVERT: A 462 MET cc_start: 0.4990 (OUTLIER) cc_final: 0.4349 (mpt) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 1.2396 time to fit residues: 65.6211 Evaluate side-chains 54 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4063 Z= 0.177 Angle : 0.562 7.956 5545 Z= 0.268 Chirality : 0.038 0.140 653 Planarity : 0.004 0.034 692 Dihedral : 3.589 26.685 574 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.39 % Allowed : 11.48 % Favored : 86.12 % 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: 2.30 (0.37), residues: 517 helix: 1.72 (0.27), residues: 365 sheet: -1.62 (1.74), residues: 10 loop : 1.57 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.007 0.000 ARG A 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.398 Fit side-chains REVERT: A 38 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: A 90 GLN cc_start: 0.8078 (mm110) cc_final: 0.7841 (mp10) REVERT: A 120 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 126 SER cc_start: 0.8525 (t) cc_final: 0.7915 (m) REVERT: A 281 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.7143 (mtm-85) REVERT: A 462 MET cc_start: 0.4866 (OUTLIER) cc_final: 0.4256 (mpt) outliers start: 10 outliers final: 3 residues processed: 47 average time/residue: 1.1769 time to fit residues: 57.6230 Evaluate side-chains 49 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 305 HIS A 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112016 restraints weight = 15040.705| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.73 r_work: 0.3107 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4063 Z= 0.155 Angle : 0.551 7.578 5545 Z= 0.260 Chirality : 0.037 0.141 653 Planarity : 0.004 0.033 692 Dihedral : 3.398 22.128 574 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.91 % Allowed : 12.20 % Favored : 85.89 % 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: 2.56 (0.38), residues: 517 helix: 1.94 (0.27), residues: 365 sheet: -1.68 (1.65), residues: 10 loop : 1.59 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 242 PHE 0.011 0.001 PHE A 358 TYR 0.023 0.002 TYR A 272 ARG 0.007 0.000 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.38 seconds wall clock time: 35 minutes 35.96 seconds (2135.96 seconds total)