Starting phenix.real_space_refine (version: dev) on Thu May 12 18:33:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a8p_11679/05_2022/7a8p_11679_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7305 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7305 Unusual residues: {'R4Q': 1} Inner-chain residues flagged as termini: ['pdbres="SER A1230 "'] Classifications: {'undetermined': 1, 'peptide': 911} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 59, 'TRANS': 851, None: 1} Not linked: pdbres="SER A1230 " pdbres="R4Q A1301 " Chain breaks: 6 Time building chain proxies: 4.60, per 1000 atoms: 0.63 Number of scatterers: 7305 At special positions: 0 Unit cell: (77.562, 97.578, 110.922, 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) Cl 1 17.00 S 46 16.00 F 1 9.00 O 1284 8.00 N 1304 7.00 C 4669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 330 through 336 removed outlier: 4.167A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.595A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 427 through 462 removed outlier: 3.719A pdb=" N ARG A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 497 through 519 Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.683A pdb=" N LYS A 532 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 689 through 703 removed outlier: 4.481A pdb=" N GLY A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 857 through 876 removed outlier: 5.336A pdb=" N ASP A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 887 No H-bonds generated for 'chain 'A' and resid 885 through 887' Processing helix chain 'A' and resid 891 through 906 Processing helix chain 'A' and resid 926 through 935 Processing helix chain 'A' and resid 938 through 943 Processing helix chain 'A' and resid 955 through 973 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 987 through 999 Processing helix chain 'A' and resid 1007 through 1017 removed outlier: 3.586A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 5.244A pdb=" N TRP A1026 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1063 Processing helix chain 'A' and resid 1114 through 1142 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1160 through 1176 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1219 through 1224 Processing sheet with id= A, first strand: chain 'A' and resid 411 through 415 Processing sheet with id= B, first strand: chain 'A' and resid 607 through 609 removed outlier: 3.515A pdb=" N TYR A 607 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 622 " --> pdb=" O TYR A 607 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 620 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 707 through 709 Processing sheet with id= D, first strand: chain 'A' and resid 919 through 921 Processing sheet with id= E, first strand: chain 'A' and resid 1069 through 1071 385 hydrogen bonds defined for protein. 1083 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: 2.42 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1746 1.33 - 1.45: 1433 1.45 - 1.57: 4230 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 7482 Sorted by residual: bond pdb=" C21 R4Q A1301 " pdb=" O20 R4Q A1301 " ideal model delta sigma weight residual 1.497 1.379 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C02 R4Q A1301 " pdb=" C23 R4Q A1301 " ideal model delta sigma weight residual 1.528 1.642 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C08 R4Q A1301 " pdb=" C17 R4Q A1301 " ideal model delta sigma weight residual 1.449 1.348 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " ideal model delta sigma weight residual 1.398 1.483 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C12 R4Q A1301 " pdb=" F13 R4Q A1301 " ideal model delta sigma weight residual 1.364 1.281 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 7477 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 309 107.13 - 113.84: 4165 113.84 - 120.54: 3103 120.54 - 127.25: 2453 127.25 - 133.95: 123 Bond angle restraints: 10153 Sorted by residual: angle pdb=" C09 R4Q A1301 " pdb=" C15 R4Q A1301 " pdb="CL1 R4Q A1301 " ideal model delta sigma weight residual 130.83 119.08 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C14 R4Q A1301 " pdb=" C15 R4Q A1301 " pdb="CL1 R4Q A1301 " ideal model delta sigma weight residual 108.34 118.39 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C23 R4Q A1301 " pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " ideal model delta sigma weight residual 109.47 117.54 -8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA PRO A 423 " pdb=" C PRO A 423 " pdb=" N SER A 424 " ideal model delta sigma weight residual 114.74 117.22 -2.48 1.03e+00 9.43e-01 5.79e+00 angle pdb=" C02 R4Q A1301 " pdb=" O03 R4Q A1301 " pdb=" C04 R4Q A1301 " ideal model delta sigma weight residual 113.90 120.18 -6.28 3.00e+00 1.11e-01 4.38e+00 ... (remaining 10148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 4141 23.04 - 46.08: 348 46.08 - 69.11: 31 69.11 - 92.15: 15 92.15 - 115.19: 1 Dihedral angle restraints: 4536 sinusoidal: 1878 harmonic: 2658 Sorted by residual: dihedral pdb=" C28 R4Q A1301 " pdb=" C26 R4Q A1301 " pdb=" C27 R4Q A1301 " pdb=" N25 R4Q A1301 " ideal model delta sinusoidal sigma weight residual 53.84 -61.35 115.19 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " pdb=" OE1 GLU A 495 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C26 R4Q A1301 " pdb=" C27 R4Q A1301 " pdb=" C28 R4Q A1301 " pdb=" C29 R4Q A1301 " ideal model delta sinusoidal sigma weight residual 53.22 -32.84 86.06 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 4533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 865 0.031 - 0.062: 178 0.062 - 0.093: 57 0.093 - 0.123: 25 0.123 - 0.154: 4 Chirality restraints: 1129 Sorted by residual: chirality pdb=" C02 R4Q A1301 " pdb=" C01 R4Q A1301 " pdb=" C23 R4Q A1301 " pdb=" O03 R4Q A1301 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" C29 R4Q A1301 " pdb=" C28 R4Q A1301 " pdb=" C30 R4Q A1301 " pdb=" C33 R4Q A1301 " both_signs ideal model delta sigma weight residual False -2.70 -2.84 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA VAL A1211 " pdb=" N VAL A1211 " pdb=" C VAL A1211 " pdb=" CB VAL A1211 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1126 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 624 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 625 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1119 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-01 pdb=" N PRO A1120 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.08e-01 pdb=" N PRO A 240 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.012 5.00e-02 4.00e+02 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 164 2.71 - 3.26: 7634 3.26 - 3.81: 12011 3.81 - 4.35: 14364 4.35 - 4.90: 24784 Nonbonded interactions: 58957 Sorted by model distance: nonbonded pdb=" O TYR A1082 " pdb=" NE2 GLN A1115 " model vdw 2.165 2.520 nonbonded pdb=" O VAL A1001 " pdb=" OG1 THR A1002 " model vdw 2.178 2.440 nonbonded pdb=" OE1 GLN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.246 2.520 nonbonded pdb=" OH TYR A 530 " pdb=" O PRO A 651 " model vdw 2.279 2.440 nonbonded pdb=" N GLU A 545 " pdb=" OE1 GLU A 545 " model vdw 2.285 2.520 ... (remaining 58952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 46 5.16 5 Cl 1 4.86 5 C 4669 2.51 5 N 1304 2.21 5 O 1284 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.390 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 0.118 7482 Z= 0.254 Angle : 0.516 11.751 10153 Z= 0.250 Chirality : 0.032 0.154 1129 Planarity : 0.003 0.034 1305 Dihedral : 16.068 115.189 2806 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.63 % 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: 0.97 (0.26), residues: 897 helix: 1.44 (0.20), residues: 585 sheet: -1.19 (0.84), residues: 32 loop : -0.77 (0.34), residues: 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 154 average time/residue: 0.1983 time to fit residues: 40.5360 Evaluate side-chains 122 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0860 time to fit residues: 1.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 488 GLN A 624 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 7482 Z= 0.229 Angle : 0.569 8.644 10153 Z= 0.277 Chirality : 0.036 0.197 1129 Planarity : 0.006 0.095 1305 Dihedral : 3.799 65.126 1002 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.15 % 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 (0.28), residues: 897 helix: 2.10 (0.21), residues: 588 sheet: -0.69 (0.90), residues: 32 loop : 0.09 (0.38), residues: 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.815 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 130 average time/residue: 0.1898 time to fit residues: 33.6644 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1291 time to fit residues: 2.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN A 921 GLN ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 7482 Z= 0.282 Angle : 0.549 9.566 10153 Z= 0.271 Chirality : 0.038 0.211 1129 Planarity : 0.006 0.081 1305 Dihedral : 4.247 80.106 1002 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 897 helix: 2.11 (0.21), residues: 587 sheet: -0.90 (0.90), residues: 32 loop : 0.20 (0.38), residues: 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.750 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 129 average time/residue: 0.1775 time to fit residues: 31.7793 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0828 time to fit residues: 2.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 624 HIS A 719 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 7482 Z= 0.249 Angle : 0.546 8.685 10153 Z= 0.271 Chirality : 0.037 0.162 1129 Planarity : 0.005 0.083 1305 Dihedral : 4.221 79.805 1002 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 897 helix: 2.17 (0.21), residues: 586 sheet: -0.71 (0.94), residues: 32 loop : 0.27 (0.38), residues: 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.895 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 122 average time/residue: 0.1921 time to fit residues: 32.8163 Evaluate side-chains 111 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0702 time to fit residues: 1.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 HIS ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 7482 Z= 0.255 Angle : 0.613 15.837 10153 Z= 0.304 Chirality : 0.036 0.157 1129 Planarity : 0.005 0.050 1305 Dihedral : 4.310 82.693 1002 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 897 helix: 2.18 (0.21), residues: 585 sheet: -0.73 (0.96), residues: 32 loop : 0.26 (0.38), residues: 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.838 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 120 average time/residue: 0.1767 time to fit residues: 29.4169 Evaluate side-chains 104 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0746 time to fit residues: 1.5663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 7482 Z= 0.246 Angle : 0.564 10.413 10153 Z= 0.279 Chirality : 0.036 0.146 1129 Planarity : 0.006 0.120 1305 Dihedral : 4.280 81.274 1002 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 897 helix: 2.22 (0.22), residues: 585 sheet: -0.78 (1.06), residues: 22 loop : 0.26 (0.37), residues: 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.866 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 120 average time/residue: 0.1888 time to fit residues: 31.2197 Evaluate side-chains 109 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0783 time to fit residues: 1.9064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 52 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: ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.208 7482 Z= 0.288 Angle : 0.585 15.024 10153 Z= 0.292 Chirality : 0.036 0.139 1129 Planarity : 0.006 0.092 1305 Dihedral : 4.329 82.396 1002 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 897 helix: 2.23 (0.22), residues: 584 sheet: -0.85 (1.09), residues: 22 loop : 0.21 (0.37), residues: 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.773 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 110 average time/residue: 0.1999 time to fit residues: 30.1980 Evaluate side-chains 101 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 624 HIS ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.462 7482 Z= 0.552 Angle : 1.102 73.900 10153 Z= 0.506 Chirality : 0.036 0.155 1129 Planarity : 0.008 0.149 1305 Dihedral : 4.361 82.224 1002 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.28), residues: 897 helix: 2.24 (0.22), residues: 584 sheet: -0.88 (1.09), residues: 22 loop : 0.23 (0.37), residues: 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.929 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.1992 time to fit residues: 28.3777 Evaluate side-chains 100 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0830 time to fit residues: 1.5373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.453 7482 Z= 0.599 Angle : 1.014 73.900 10153 Z= 0.428 Chirality : 0.036 0.165 1129 Planarity : 0.006 0.118 1305 Dihedral : 4.354 82.224 1002 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 897 helix: 2.25 (0.22), residues: 584 sheet: -0.88 (1.09), residues: 22 loop : 0.18 (0.37), residues: 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.867 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 0.2010 time to fit residues: 28.0908 Evaluate side-chains 102 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0678 time to fit residues: 1.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.453 7482 Z= 0.598 Angle : 1.017 73.900 10153 Z= 0.432 Chirality : 0.036 0.165 1129 Planarity : 0.006 0.118 1305 Dihedral : 4.354 82.224 1002 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 897 helix: 2.25 (0.22), residues: 584 sheet: -0.88 (1.09), residues: 22 loop : 0.18 (0.37), residues: 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.931 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2119 time to fit residues: 28.8513 Evaluate side-chains 100 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121005 restraints weight = 9057.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119775 restraints weight = 7333.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121726 restraints weight = 6888.316| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.453 7482 Z= 0.598 Angle : 1.017 73.900 10153 Z= 0.432 Chirality : 0.036 0.165 1129 Planarity : 0.006 0.118 1305 Dihedral : 4.354 82.224 1002 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 897 helix: 2.25 (0.22), residues: 584 sheet: -0.88 (1.09), residues: 22 loop : 0.18 (0.37), residues: 291 =============================================================================== Job complete usr+sys time: 1463.03 seconds wall clock time: 27 minutes 17.66 seconds (1637.66 seconds total)