null Sun 23 Dec 22:22:55 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 2oc5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-4.0-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/2oc5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-4.0-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 ============================================================ Sun 23 Dec 22:23:04 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/2oc5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-4.0-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 214 and 0 Target number of residues in the AU: 214 Target solvent content: 0.6693 Checking the provided sequence file Detected sequence length: 244 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 244 Adjusted target solvent content: 0.62 Input MTZ file: 2oc5-4.0-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: 96 Cell parameters: 77.390 77.390 116.960 90.000 90.000 90.000 Input sequence file: 2oc5-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1952 target number of atoms Had to go as low as 0.65 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 3 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.240 4.001 Wilson plot Bfac: 91.29 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3268 reflections ( 98.88 % complete ) and 0 restraints for refining 2164 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3308 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3371 (Rfree = 0.000) for 2164 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.38 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward Round 1: 100 peptides, 17 chains. Longest chain 9 peptides. Score 0.349 Round 2: 115 peptides, 14 chains. Longest chain 19 peptides. Score 0.483 Round 3: 119 peptides, 13 chains. Longest chain 18 peptides. Score 0.520 Round 4: 117 peptides, 13 chains. Longest chain 15 peptides. Score 0.512 Round 5: 115 peptides, 13 chains. Longest chain 16 peptides. Score 0.503 Taking the results from Round 3 Chains 13, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4270 restraints for refining 1760 atoms. 3859 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2519 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 2: After refmac, R = 0.2366 (Rfree = 0.000) for 1722 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 1693 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2236 (Rfree = 0.000) for 1677 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2210 (Rfree = 0.000) for 1669 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 3.30 Search for helices and strands: 0 residues in 0 chains, 1770 seeds are put forward Round 1: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.396 Round 2: 112 peptides, 16 chains. Longest chain 12 peptides. Score 0.429 Round 3: 119 peptides, 14 chains. Longest chain 17 peptides. Score 0.500 Round 4: 119 peptides, 15 chains. Longest chain 13 peptides. Score 0.481 Round 5: 118 peptides, 12 chains. Longest chain 25 peptides. Score 0.535 Taking the results from Round 5 Chains 12, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4005 restraints for refining 1721 atoms. 3593 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2601 (Rfree = 0.000) for 1721 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.2452 (Rfree = 0.000) for 1696 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.2370 (Rfree = 0.000) for 1687 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2343 (Rfree = 0.000) for 1677 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 1677 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.25 Search for helices and strands: 0 residues in 0 chains, 1777 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.415 Round 2: 117 peptides, 14 chains. Longest chain 18 peptides. Score 0.492 Round 3: 118 peptides, 13 chains. Longest chain 19 peptides. Score 0.516 Round 4: 114 peptides, 12 chains. Longest chain 24 peptides. Score 0.519 Round 5: 113 peptides, 11 chains. Longest chain 19 peptides. Score 0.535 Taking the results from Round 5 Chains 12, Residues 102, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 3977 restraints for refining 1762 atoms. 3556 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2555 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 12: After refmac, R = 0.2388 (Rfree = 0.000) for 1739 atoms. Found 7 (8 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2298 (Rfree = 0.000) for 1727 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2255 (Rfree = 0.000) for 1725 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2243 (Rfree = 0.000) for 1719 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.90 3.31 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 116 peptides, 16 chains. Longest chain 17 peptides. Score 0.447 Round 2: 120 peptides, 15 chains. Longest chain 16 peptides. Score 0.485 Round 3: 133 peptides, 15 chains. Longest chain 17 peptides. Score 0.538 Round 4: 124 peptides, 14 chains. Longest chain 18 peptides. Score 0.521 Round 5: 123 peptides, 12 chains. Longest chain 30 peptides. Score 0.555 Taking the results from Round 5 Chains 12, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4158 restraints for refining 1763 atoms. 3726 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2614 (Rfree = 0.000) for 1763 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 17: After refmac, R = 0.2333 (Rfree = 0.000) for 1745 atoms. Found 2 (8 requested) and removed 18 (4 requested) atoms. Cycle 18: After refmac, R = 0.2306 (Rfree = 0.000) for 1723 atoms. Found 3 (8 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 1711 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 1706 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.90 3.31 Search for helices and strands: 0 residues in 0 chains, 1779 seeds are put forward Round 1: 111 peptides, 16 chains. Longest chain 18 peptides. Score 0.424 Round 2: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.410 Round 3: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.443 Round 4: 115 peptides, 17 chains. Longest chain 16 peptides. Score 0.422 Round 5: 122 peptides, 18 chains. Longest chain 17 peptides. Score 0.433 Taking the results from Round 3 Chains 16, Residues 99, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4041 restraints for refining 1762 atoms. 3628 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2675 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 22: After refmac, R = 0.2428 (Rfree = 0.000) for 1749 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2326 (Rfree = 0.000) for 1741 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2314 (Rfree = 0.000) for 1739 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2275 (Rfree = 0.000) for 1728 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.34 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.328 Round 2: 114 peptides, 14 chains. Longest chain 17 peptides. Score 0.479 Round 3: 116 peptides, 16 chains. Longest chain 14 peptides. Score 0.447 Round 4: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.445 Round 5: 116 peptides, 14 chains. Longest chain 14 peptides. Score 0.488 Taking the results from Round 5 Chains 14, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4104 restraints for refining 1762 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2473 (Rfree = 0.000) for 1762 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 27: After refmac, R = 0.2389 (Rfree = 0.000) for 1740 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2449 (Rfree = 0.000) for 1734 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2438 (Rfree = 0.000) for 1723 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2439 (Rfree = 0.000) for 1711 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.94 3.35 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.306 Round 2: 118 peptides, 18 chains. Longest chain 14 peptides. Score 0.415 Round 3: 129 peptides, 17 chains. Longest chain 20 peptides. Score 0.484 Round 4: 124 peptides, 20 chains. Longest chain 11 peptides. Score 0.402 Round 5: 123 peptides, 18 chains. Longest chain 13 peptides. Score 0.438 Taking the results from Round 3 Chains 17, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4153 restraints for refining 1763 atoms. 3722 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2410 (Rfree = 0.000) for 1763 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 32: After refmac, R = 0.2253 (Rfree = 0.000) for 1735 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2221 (Rfree = 0.000) for 1728 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2201 (Rfree = 0.000) for 1720 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2234 (Rfree = 0.000) for 1704 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.95 3.36 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward Round 1: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.300 Round 2: 106 peptides, 16 chains. Longest chain 15 peptides. Score 0.401 Round 3: 103 peptides, 15 chains. Longest chain 15 peptides. Score 0.408 Round 4: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.391 Round 5: 111 peptides, 14 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 5 Chains 15, Residues 97, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4031 restraints for refining 1762 atoms. 3605 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2418 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 37: After refmac, R = 0.2293 (Rfree = 0.000) for 1741 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2218 (Rfree = 0.000) for 1731 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 1727 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2168 (Rfree = 0.000) for 1723 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.94 3.35 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.283 Round 2: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Round 3: 119 peptides, 16 chains. Longest chain 17 peptides. Score 0.460 Round 4: 114 peptides, 16 chains. Longest chain 14 peptides. Score 0.438 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 3 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3268 reflections ( 98.88 % complete ) and 4097 restraints for refining 1763 atoms. 3701 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2383 (Rfree = 0.000) for 1763 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2280 (Rfree = 0.000) for 1748 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2304 (Rfree = 0.000) for 1740 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2239 (Rfree = 0.000) for 1732 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2227 (Rfree = 0.000) for 1724 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.33 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.249 Round 2: 102 peptides, 18 chains. Longest chain 12 peptides. Score 0.337 Round 3: 111 peptides, 18 chains. Longest chain 16 peptides. Score 0.382 Round 4: 110 peptides, 18 chains. Longest chain 10 peptides. Score 0.377 Round 5: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.328 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 93, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2oc5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3268 reflections ( 98.88 % complete ) and 4147 restraints for refining 1763 atoms. 3781 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2398 (Rfree = 0.000) for 1763 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2325 (Rfree = 0.000) for 1753 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2296 (Rfree = 0.000) for 1744 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2288 (Rfree = 0.000) for 1739 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:30 GMT 2018 Job finished. TimeTaking 31.58 Used memory is bytes: 2819720