Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fur-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fur-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:04 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 372 and 0 Target number of residues in the AU: 372 Target solvent content: 0.5051 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-1.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.473 1.798 Wilson plot Bfac: 24.57 38188 reflections ( 99.31 % complete ) and 0 restraints for refining 3705 atoms. Observations/parameters ratio is 2.58 ------------------------------------------------------ Starting model: R = 0.3320 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2868 (Rfree = 0.000) for 3705 atoms. Found 89 (171 requested) and removed 96 (85 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.10 2.28 NCS extension: 0 residues added, 3698 seeds are put forward Round 1: 292 peptides, 26 chains. Longest chain 25 peptides. Score 0.780 Round 2: 322 peptides, 19 chains. Longest chain 41 peptides. Score 0.869 Round 3: 342 peptides, 10 chains. Longest chain 83 peptides. Score 0.928 Round 4: 360 peptides, 8 chains. Longest chain 115 peptides. Score 0.945 Round 5: 367 peptides, 8 chains. Longest chain 128 peptides. Score 0.948 Taking the results from Round 5 Chains 10, Residues 359, Estimated correctness of the model 99.8 % 6 chains (324 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 146 B and 150 B 8 chains (364 residues) following loop building 4 chains (329 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3590 restraints for refining 3315 atoms. 792 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2937 (Rfree = 0.000) for 3315 atoms. Found 87 (154 requested) and removed 84 (77 requested) atoms. Cycle 2: After refmac, R = 0.2577 (Rfree = 0.000) for 3312 atoms. Found 95 (150 requested) and removed 35 (76 requested) atoms. Cycle 3: After refmac, R = 0.2412 (Rfree = 0.000) for 3361 atoms. Found 86 (153 requested) and removed 20 (78 requested) atoms. Cycle 4: After refmac, R = 0.2295 (Rfree = 0.000) for 3415 atoms. Found 67 (156 requested) and removed 36 (79 requested) atoms. Cycle 5: After refmac, R = 0.2227 (Rfree = 0.000) for 3443 atoms. Found 74 (153 requested) and removed 23 (79 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 2.17 NCS extension: 45 residues added (118 deleted due to clashes), 3540 seeds are put forward Round 1: 376 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 2: 379 peptides, 4 chains. Longest chain 166 peptides. Score 0.965 Round 3: 380 peptides, 4 chains. Longest chain 192 peptides. Score 0.965 Round 4: 381 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Round 5: 381 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Taking the results from Round 5 Chains 3, Residues 378, Estimated correctness of the model 99.9 % 3 chains (378 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 157 B and 160 B 2 chains (380 residues) following loop building 2 chains (380 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3286 restraints for refining 3445 atoms. 229 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2293 (Rfree = 0.000) for 3445 atoms. Found 116 (153 requested) and removed 78 (79 requested) atoms. Cycle 7: After refmac, R = 0.2189 (Rfree = 0.000) for 3482 atoms. Found 89 (151 requested) and removed 35 (80 requested) atoms. Cycle 8: After refmac, R = 0.2086 (Rfree = 0.000) for 3530 atoms. Found 84 (154 requested) and removed 27 (82 requested) atoms. Cycle 9: After refmac, R = 0.2008 (Rfree = 0.000) for 3586 atoms. Found 76 (156 requested) and removed 27 (83 requested) atoms. Cycle 10: After refmac, R = 0.1958 (Rfree = 0.000) for 3630 atoms. Found 74 (158 requested) and removed 49 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3655 seeds are put forward Round 1: 375 peptides, 4 chains. Longest chain 168 peptides. Score 0.964 Round 2: 378 peptides, 2 chains. Longest chain 191 peptides. Score 0.970 Round 3: 377 peptides, 6 chains. Longest chain 142 peptides. Score 0.958 Round 4: 373 peptides, 6 chains. Longest chain 161 peptides. Score 0.957 Round 5: 378 peptides, 5 chains. Longest chain 142 peptides. Score 0.962 Taking the results from Round 2 Chains 2, Residues 376, Estimated correctness of the model 99.9 % 2 chains (376 residues) have been docked in sequence Building loops using Loopy2018 2 chains (376 residues) following loop building 2 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3338 restraints for refining 3495 atoms. 313 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2104 (Rfree = 0.000) for 3495 atoms. Found 133 (149 requested) and removed 57 (81 requested) atoms. Cycle 12: After refmac, R = 0.2050 (Rfree = 0.000) for 3567 atoms. Found 82 (152 requested) and removed 71 (82 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 3576 atoms. Found 102 (149 requested) and removed 40 (83 requested) atoms. Cycle 14: After refmac, R = 0.1941 (Rfree = 0.000) for 3634 atoms. Found 80 (151 requested) and removed 66 (84 requested) atoms. Cycle 15: After refmac, R = 0.1913 (Rfree = 0.000) for 3642 atoms. Found 96 (149 requested) and removed 66 (84 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.99 2.16 NCS extension: 3 residues added (1 deleted due to clashes), 3675 seeds are put forward Round 1: 378 peptides, 2 chains. Longest chain 191 peptides. Score 0.970 Round 2: 376 peptides, 3 chains. Longest chain 191 peptides. Score 0.967 Round 3: 373 peptides, 4 chains. Longest chain 153 peptides. Score 0.963 Round 4: 374 peptides, 6 chains. Longest chain 110 peptides. Score 0.957 Round 5: 369 peptides, 7 chains. Longest chain 122 peptides. Score 0.952 Taking the results from Round 1 Chains 2, Residues 376, Estimated correctness of the model 99.9 % 2 chains (376 residues) have been docked in sequence Building loops using Loopy2018 2 chains (376 residues) following loop building 2 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3335 restraints for refining 3495 atoms. 310 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2054 (Rfree = 0.000) for 3495 atoms. Found 131 (139 requested) and removed 55 (81 requested) atoms. Cycle 17: After refmac, R = 0.1984 (Rfree = 0.000) for 3568 atoms. Found 76 (142 requested) and removed 60 (82 requested) atoms. Cycle 18: After refmac, R = 0.1944 (Rfree = 0.000) for 3578 atoms. Found 99 (139 requested) and removed 38 (83 requested) atoms. Cycle 19: After refmac, R = 0.1907 (Rfree = 0.000) for 3636 atoms. Found 86 (141 requested) and removed 63 (84 requested) atoms. Cycle 20: After refmac, R = 0.1893 (Rfree = 0.000) for 3655 atoms. Found 103 (139 requested) and removed 58 (84 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 2.16 NCS extension: 2 residues added (2 deleted due to clashes), 3702 seeds are put forward Round 1: 381 peptides, 2 chains. Longest chain 192 peptides. Score 0.971 Round 2: 380 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 3: 380 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 4: 379 peptides, 3 chains. Longest chain 189 peptides. Score 0.968 Round 5: 376 peptides, 6 chains. Longest chain 170 peptides. Score 0.958 Taking the results from Round 3 Chains 2, Residues 378, Estimated correctness of the model 99.9 % 2 chains (378 residues) have been docked in sequence Building loops using Loopy2018 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3293 restraints for refining 3499 atoms. 254 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2039 (Rfree = 0.000) for 3499 atoms. Found 130 (130 requested) and removed 56 (81 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1968 (Rfree = 0.000) for 3571 atoms. Found 104 (132 requested) and removed 61 (82 requested) atoms. Cycle 23: After refmac, R = 0.1924 (Rfree = 0.000) for 3608 atoms. Found 108 (130 requested) and removed 67 (83 requested) atoms. Cycle 24: After refmac, R = 0.1925 (Rfree = 0.000) for 3646 atoms. Found 98 (128 requested) and removed 79 (84 requested) atoms. Cycle 25: After refmac, R = 0.1897 (Rfree = 0.000) for 3662 atoms. Found 111 (126 requested) and removed 79 (85 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.98 2.15 NCS extension: 0 residues added, 3694 seeds are put forward Round 1: 376 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 2: 379 peptides, 2 chains. Longest chain 190 peptides. Score 0.971 Round 3: 376 peptides, 5 chains. Longest chain 166 peptides. Score 0.961 Round 4: 375 peptides, 4 chains. Longest chain 190 peptides. Score 0.964 Round 5: 379 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 2 Chains 2, Residues 377, Estimated correctness of the model 99.9 % 2 chains (377 residues) have been docked in sequence Building loops using Loopy2018 2 chains (377 residues) following loop building 2 chains (377 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3344 restraints for refining 3522 atoms. 311 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2130 (Rfree = 0.000) for 3522 atoms. Found 113 (117 requested) and removed 76 (81 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 3557 atoms. Found 104 (115 requested) and removed 52 (82 requested) atoms. Cycle 28: After refmac, R = 0.1966 (Rfree = 0.000) for 3605 atoms. Found 100 (117 requested) and removed 69 (83 requested) atoms. Cycle 29: After refmac, R = 0.1941 (Rfree = 0.000) for 3635 atoms. Found 107 (114 requested) and removed 68 (84 requested) atoms. Cycle 30: After refmac, R = 0.1919 (Rfree = 0.000) for 3673 atoms. Found 93 (112 requested) and removed 78 (85 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.98 2.15 NCS extension: 0 residues added, 3688 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 166 peptides. Score 0.963 Round 2: 378 peptides, 2 chains. Longest chain 190 peptides. Score 0.970 Round 3: 376 peptides, 5 chains. Longest chain 190 peptides. Score 0.961 Round 4: 377 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 5: 375 peptides, 8 chains. Longest chain 140 peptides. Score 0.951 Taking the results from Round 2 Chains 2, Residues 376, Estimated correctness of the model 99.9 % 2 chains (376 residues) have been docked in sequence Building loops using Loopy2018 2 chains (376 residues) following loop building 2 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3333 restraints for refining 3513 atoms. 306 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2090 (Rfree = 0.000) for 3513 atoms. Found 104 (104 requested) and removed 71 (81 requested) atoms. Cycle 32: After refmac, R = 0.1987 (Rfree = 0.000) for 3542 atoms. Found 102 (102 requested) and removed 32 (82 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 3610 atoms. Found 83 (104 requested) and removed 56 (83 requested) atoms. Cycle 34: After refmac, R = 0.1893 (Rfree = 0.000) for 3635 atoms. Found 94 (101 requested) and removed 59 (84 requested) atoms. Cycle 35: After refmac, R = 0.1884 (Rfree = 0.000) for 3670 atoms. Found 88 (99 requested) and removed 76 (85 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3682 seeds are put forward Round 1: 375 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 2: 375 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 3: 372 peptides, 8 chains. Longest chain 74 peptides. Score 0.950 Round 4: 376 peptides, 5 chains. Longest chain 162 peptides. Score 0.961 Round 5: 370 peptides, 6 chains. Longest chain 133 peptides. Score 0.956 Taking the results from Round 2 Chains 6, Residues 371, Estimated correctness of the model 99.9 % 5 chains (368 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 44 A Built loop between residues 153 B and 159 B 3 chains (376 residues) following loop building 3 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3295 restraints for refining 3481 atoms. 273 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2063 (Rfree = 0.000) for 3481 atoms. Found 90 (90 requested) and removed 57 (80 requested) atoms. Cycle 37: After refmac, R = 0.1961 (Rfree = 0.000) for 3513 atoms. Found 88 (88 requested) and removed 39 (81 requested) atoms. Cycle 38: After refmac, R = 0.1905 (Rfree = 0.000) for 3559 atoms. Found 89 (89 requested) and removed 37 (82 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1890 (Rfree = 0.000) for 3609 atoms. Found 85 (90 requested) and removed 56 (83 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1853 (Rfree = 0.000) for 3636 atoms. Found 87 (87 requested) and removed 59 (84 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.00 2.17 NCS extension: 56 residues added (133 deleted due to clashes), 3722 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 165 peptides. Score 0.963 Round 2: 378 peptides, 3 chains. Longest chain 188 peptides. Score 0.968 Round 3: 378 peptides, 5 chains. Longest chain 161 peptides. Score 0.962 Round 4: 380 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Round 5: 381 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Taking the results from Round 5 Chains 4, Residues 378, Estimated correctness of the model 99.9 % 3 chains (377 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 179 A and 182 A 3 chains (380 residues) following loop building 2 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3261 restraints for refining 3497 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2007 (Rfree = 0.000) for 3497 atoms. Found 81 (81 requested) and removed 52 (81 requested) atoms. Cycle 42: After refmac, R = 0.1927 (Rfree = 0.000) for 3524 atoms. Found 81 (81 requested) and removed 41 (81 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1871 (Rfree = 0.000) for 3563 atoms. Found 82 (82 requested) and removed 41 (82 requested) atoms. Cycle 44: After refmac, R = 0.1852 (Rfree = 0.000) for 3602 atoms. Found 83 (83 requested) and removed 56 (83 requested) atoms. Cycle 45: After refmac, R = 0.1854 (Rfree = 0.000) for 3627 atoms. Found 84 (84 requested) and removed 61 (84 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3651 seeds are put forward Round 1: 378 peptides, 4 chains. Longest chain 167 peptides. Score 0.965 Round 2: 380 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 3: 373 peptides, 9 chains. Longest chain 117 peptides. Score 0.947 Round 4: 375 peptides, 6 chains. Longest chain 167 peptides. Score 0.958 Round 5: 381 peptides, 3 chains. Longest chain 192 peptides. Score 0.968 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 378, Estimated correctness of the model 99.9 % 3 chains (376 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 115 A and 118 A 3 chains (380 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38188 reflections ( 99.31 % complete ) and 3047 restraints for refining 2985 atoms. Observations/parameters ratio is 3.20 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 2985 atoms. Found 67 (69 requested) and removed 0 (69 requested) atoms. Cycle 47: After refmac, R = 0.2341 (Rfree = 0.000) for 2985 atoms. Found 26 (70 requested) and removed 0 (70 requested) atoms. Cycle 48: After refmac, R = 0.2219 (Rfree = 0.000) for 2985 atoms. Found 15 (71 requested) and removed 0 (71 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2155 (Rfree = 0.000) for 2985 atoms. Found 15 (71 requested) and removed 2 (71 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:32:48 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 64.88