Starting phenix.real_space_refine on Wed Jun 26 12:29:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4o_45192/06_2024/9c4o_45192_trim_updated.pdb" } resolution = 1.99 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= 0.064 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 19 5.16 5 C 3205 2.51 5 N 915 2.21 5 O 1143 1.98 5 H 4883 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 85": "OD1" <-> "OD2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 10030 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 633} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 136 Unusual residues: {' CA': 1, 'PQQ': 1} Classifications: {'undetermined': 2, 'water': 111} Link IDs: {None: 112} Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10166 At special positions: 0 Unit cell: (86.92, 62.32, 72.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 19 16.00 O 1143 8.00 N 915 7.00 C 3205 6.00 H 4883 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 585 " 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: 8.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 6 sheets defined 4.7% alpha, 52.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 No H-bonds generated for 'chain 'A' and resid 52 through 55' Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 51 removed outlier: 7.104A pdb=" N THR A 155 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 133 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN A 153 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 135 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 151 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 77 Processing sheet with id= C, first strand: chain 'A' and resid 176 through 184 removed outlier: 3.528A pdb=" N PHE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE A 471 " --> pdb=" O TRP A 447 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N TRP A 447 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY A 367 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 389 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG A 365 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 391 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A 363 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 393 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET A 361 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A 395 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 397 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN A 357 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 355 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 401 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 353 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 403 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 351 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP A 405 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 371 through 373 Processing sheet with id= E, first strand: chain 'A' and resid 526 through 533 removed outlier: 6.741A pdb=" N THR A 538 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 532 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 668 through 671 removed outlier: 7.098A pdb=" N GLU A 682 " --> pdb=" O GLY A 669 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 801 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: 4.42 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4883 1.03 - 1.23: 15 1.23 - 1.42: 2322 1.42 - 1.62: 2914 1.62 - 1.81: 36 Bond restraints: 10170 Sorted by residual: bond pdb=" C PRO A 683 " pdb=" N SER A 684 " ideal model delta sigma weight residual 1.327 1.308 0.018 1.71e-02 3.42e+03 1.16e+00 bond pdb=" CA LYS A 277 " pdb=" C LYS A 277 " ideal model delta sigma weight residual 1.526 1.515 0.011 1.08e-02 8.57e+03 1.03e+00 bond pdb=" C ALA A 450 " pdb=" N GLY A 451 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.32e-02 5.74e+03 9.14e-01 bond pdb=" C GLU A 363 " pdb=" N ASN A 364 " ideal model delta sigma weight residual 1.331 1.318 0.013 1.40e-02 5.10e+03 8.48e-01 bond pdb=" C ARG A 589 " pdb=" N MET A 590 " ideal model delta sigma weight residual 1.326 1.309 0.017 1.84e-02 2.95e+03 8.42e-01 ... (remaining 10165 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.06: 116 106.06 - 113.05: 11295 113.05 - 120.03: 3103 120.03 - 127.01: 3617 127.01 - 133.99: 73 Bond angle restraints: 18204 Sorted by residual: angle pdb=" N GLY A 492 " pdb=" CA GLY A 492 " pdb=" C GLY A 492 " ideal model delta sigma weight residual 114.67 111.15 3.52 1.10e+00 8.26e-01 1.02e+01 angle pdb=" N ASP A 530 " pdb=" CA ASP A 530 " pdb=" C ASP A 530 " ideal model delta sigma weight residual 111.24 108.22 3.02 1.29e+00 6.01e-01 5.48e+00 angle pdb=" N SER A 375 " pdb=" CA SER A 375 " pdb=" C SER A 375 " ideal model delta sigma weight residual 112.12 108.99 3.13 1.34e+00 5.57e-01 5.46e+00 angle pdb=" N PRO A 685 " pdb=" CA PRO A 685 " pdb=" C PRO A 685 " ideal model delta sigma weight residual 112.47 116.85 -4.38 2.06e+00 2.36e-01 4.52e+00 angle pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 117.33 119.30 -1.97 1.01e+00 9.80e-01 3.82e+00 ... (remaining 18199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4301 17.76 - 35.52: 360 35.52 - 53.28: 114 53.28 - 71.04: 37 71.04 - 88.80: 16 Dihedral angle restraints: 4828 sinusoidal: 2618 harmonic: 2210 Sorted by residual: dihedral pdb=" CA TYR A 680 " pdb=" C TYR A 680 " pdb=" N TYR A 681 " pdb=" CA TYR A 681 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO A 685 " pdb=" C PRO A 685 " pdb=" N GLY A 686 " pdb=" CA GLY A 686 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP A 398 " pdb=" C ASP A 398 " pdb=" N PRO A 399 " pdb=" CA PRO A 399 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 454 0.034 - 0.068: 216 0.068 - 0.102: 45 0.102 - 0.137: 29 0.137 - 0.171: 1 Chirality restraints: 745 Sorted by residual: chirality pdb=" CA PRO A 685 " pdb=" N PRO A 685 " pdb=" C PRO A 685 " pdb=" CB PRO A 685 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 742 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 684 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 685 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 685 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 685 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " 0.114 9.50e-02 1.11e+02 3.82e-02 1.62e+00 pdb=" NE ARG A 91 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 91 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 91 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 192 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 193 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.017 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 710 2.18 - 2.79: 21055 2.79 - 3.39: 30415 3.39 - 4.00: 43614 4.00 - 4.60: 63098 Nonbonded interactions: 158892 Sorted by model distance: nonbonded pdb=" O LEU A 479 " pdb=" H ASN A 490 " model vdw 1.575 1.850 nonbonded pdb=" HH TYR A 481 " pdb=" O2B PQQ A 802 " model vdw 1.583 1.850 nonbonded pdb=" HH TYR A 464 " pdb=" OE2 GLU A 502 " model vdw 1.607 1.850 nonbonded pdb=" O VAL A 638 " pdb=" H LEU A 662 " model vdw 1.616 1.850 nonbonded pdb="HD21 ASN A 357 " pdb=" OE2 GLU A 359 " model vdw 1.627 1.850 ... (remaining 158887 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: 2.420 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: 0.140 Extract box with map and model: 7.130 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.960 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 5287 Z= 0.280 Angle : 0.647 6.461 7177 Z= 0.367 Chirality : 0.044 0.171 745 Planarity : 0.005 0.051 958 Dihedral : 16.532 88.799 1925 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.18 % Allowed : 14.76 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.32), residues: 659 helix: -1.84 (0.64), residues: 47 sheet: 0.18 (0.25), residues: 349 loop : 0.34 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.016 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8545 (mmp) cc_final: 0.8331 (mmp) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 2.5496 time to fit residues: 231.3823 Evaluate side-chains 84 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5287 Z= 0.235 Angle : 0.572 6.432 7177 Z= 0.313 Chirality : 0.043 0.167 745 Planarity : 0.004 0.046 958 Dihedral : 6.666 72.698 746 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.11 % Allowed : 13.47 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.32), residues: 659 helix: -1.71 (0.66), residues: 46 sheet: 0.16 (0.25), residues: 350 loop : 0.47 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.001 0.001 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.003 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8666 (mmp) cc_final: 0.8220 (mmp) REVERT: A 576 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7495 (mmp-170) REVERT: A 595 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7376 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 2.5896 time to fit residues: 232.3833 Evaluate side-chains 85 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5287 Z= 0.298 Angle : 0.609 6.238 7177 Z= 0.335 Chirality : 0.043 0.182 745 Planarity : 0.005 0.048 958 Dihedral : 6.925 74.116 746 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.29 % Allowed : 13.47 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.09 (0.32), residues: 659 helix: -1.92 (0.63), residues: 47 sheet: 0.30 (0.26), residues: 349 loop : 0.36 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS A 342 PHE 0.020 0.002 PHE A 352 TYR 0.019 0.002 TYR A 681 ARG 0.003 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8704 (mmp) cc_final: 0.8178 (mmp) REVERT: A 595 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7391 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 86 average time/residue: 2.5511 time to fit residues: 228.8784 Evaluate side-chains 87 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 647 ASN A 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5287 Z= 0.218 Angle : 0.557 6.421 7177 Z= 0.304 Chirality : 0.043 0.161 745 Planarity : 0.004 0.043 958 Dihedral : 6.620 71.971 746 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.92 % Allowed : 14.21 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.09 (0.32), residues: 659 helix: -1.68 (0.67), residues: 46 sheet: 0.18 (0.26), residues: 350 loop : 0.49 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.001 0.001 HIS A 322 PHE 0.018 0.002 PHE A 352 TYR 0.015 0.001 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8735 (mmp) cc_final: 0.8247 (mmp) REVERT: A 377 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6464 (mpt) REVERT: A 595 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7369 (ttp-170) REVERT: A 645 LYS cc_start: 0.8543 (mtmm) cc_final: 0.7955 (mtmp) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 2.6125 time to fit residues: 231.3925 Evaluate side-chains 82 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5287 Z= 0.321 Angle : 0.623 7.075 7177 Z= 0.343 Chirality : 0.043 0.189 745 Planarity : 0.005 0.049 958 Dihedral : 6.988 73.970 746 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.92 % Allowed : 14.21 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 659 helix: -2.01 (0.62), residues: 47 sheet: 0.36 (0.26), residues: 344 loop : 0.39 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.020 0.003 PHE A 352 TYR 0.019 0.002 TYR A 681 ARG 0.004 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8740 (mmp) cc_final: 0.8349 (mmp) REVERT: A 595 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7379 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 2.8184 time to fit residues: 243.5312 Evaluate side-chains 83 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5287 Z= 0.178 Angle : 0.533 6.130 7177 Z= 0.289 Chirality : 0.044 0.149 745 Planarity : 0.004 0.034 958 Dihedral : 6.421 69.629 746 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.55 % Allowed : 14.58 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.20 (0.32), residues: 659 helix: -1.18 (0.76), residues: 40 sheet: 0.14 (0.26), residues: 350 loop : 0.60 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.001 0.000 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.013 0.001 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8719 (mmp) cc_final: 0.8159 (mmp) REVERT: A 379 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: A 595 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7336 (ttp-170) REVERT: A 645 LYS cc_start: 0.8517 (mtmm) cc_final: 0.7926 (mtmp) outliers start: 3 outliers final: 2 residues processed: 87 average time/residue: 2.5666 time to fit residues: 232.8333 Evaluate side-chains 85 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5287 Z= 0.265 Angle : 0.582 6.878 7177 Z= 0.318 Chirality : 0.043 0.178 745 Planarity : 0.005 0.045 958 Dihedral : 6.720 71.787 746 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.92 % Allowed : 14.58 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.24 (0.32), residues: 659 helix: -1.34 (0.74), residues: 40 sheet: 0.26 (0.26), residues: 349 loop : 0.53 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.019 0.002 PHE A 352 TYR 0.016 0.002 TYR A 681 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8726 (mmp) cc_final: 0.8298 (mmp) REVERT: A 595 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7366 (ttp-170) REVERT: A 645 LYS cc_start: 0.8565 (mtmm) cc_final: 0.7974 (mtmp) outliers start: 5 outliers final: 2 residues processed: 83 average time/residue: 2.7832 time to fit residues: 240.3088 Evaluate side-chains 82 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5287 Z= 0.193 Angle : 0.541 6.577 7177 Z= 0.293 Chirality : 0.043 0.156 745 Planarity : 0.004 0.037 958 Dihedral : 6.057 69.683 743 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.74 % Allowed : 14.39 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.22 (0.32), residues: 659 helix: -1.12 (0.76), residues: 40 sheet: 0.16 (0.26), residues: 350 loop : 0.60 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 568 HIS 0.001 0.000 HIS A 342 PHE 0.017 0.002 PHE A 352 TYR 0.014 0.001 TYR A 681 ARG 0.004 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8727 (mmp) cc_final: 0.8293 (mmp) REVERT: A 379 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: A 595 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7325 (ttp-170) REVERT: A 645 LYS cc_start: 0.8527 (mtmm) cc_final: 0.7937 (mtmp) outliers start: 4 outliers final: 1 residues processed: 84 average time/residue: 2.5133 time to fit residues: 220.6441 Evaluate side-chains 82 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5287 Z= 0.293 Angle : 0.604 7.246 7177 Z= 0.330 Chirality : 0.043 0.184 745 Planarity : 0.005 0.049 958 Dihedral : 6.446 72.454 743 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.74 % Allowed : 14.39 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.32), residues: 659 helix: -1.59 (0.70), residues: 41 sheet: 0.32 (0.26), residues: 344 loop : 0.50 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 322 PHE 0.020 0.003 PHE A 352 TYR 0.018 0.002 TYR A 681 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6499 (mt-10) REVERT: A 115 MET cc_start: 0.8736 (mmp) cc_final: 0.8293 (mmp) REVERT: A 595 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7364 (ttp-170) REVERT: A 645 LYS cc_start: 0.8571 (mtmm) cc_final: 0.7979 (mtmp) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 2.7721 time to fit residues: 233.3716 Evaluate side-chains 81 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5287 Z= 0.271 Angle : 0.594 7.227 7177 Z= 0.324 Chirality : 0.043 0.174 745 Planarity : 0.005 0.045 958 Dihedral : 6.413 72.013 743 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.55 % Allowed : 14.39 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.24 (0.32), residues: 659 helix: -1.62 (0.71), residues: 41 sheet: 0.31 (0.26), residues: 344 loop : 0.49 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.002 0.001 HIS A 445 PHE 0.019 0.002 PHE A 352 TYR 0.017 0.002 TYR A 681 ARG 0.004 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 515 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8738 (mmp) cc_final: 0.8296 (mmp) REVERT: A 595 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7360 (ttp-170) REVERT: A 645 LYS cc_start: 0.8566 (mtmm) cc_final: 0.7975 (mtmp) outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 2.7342 time to fit residues: 233.3926 Evaluate side-chains 84 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 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 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136406 restraints weight = 11545.862| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 0.98 r_work: 0.3590 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5287 Z= 0.211 Angle : 0.555 6.873 7177 Z= 0.301 Chirality : 0.043 0.158 745 Planarity : 0.004 0.040 958 Dihedral : 6.152 69.932 743 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.37 % Allowed : 14.39 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.11 (0.32), residues: 659 helix: -1.72 (0.67), residues: 46 sheet: 0.20 (0.26), residues: 350 loop : 0.51 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.003 0.001 HIS A 649 PHE 0.017 0.002 PHE A 352 TYR 0.014 0.001 TYR A 681 ARG 0.004 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5233.40 seconds wall clock time: 90 minutes 31.30 seconds (5431.30 seconds total)