Sun 23 Dec 22:22:43 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 2itb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-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/2itb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-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 22:22:53 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/2itb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-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 236 and 0 Target number of residues in the AU: 236 Target solvent content: 0.6471 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-3.6-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: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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 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: 53.913 3.600 Wilson plot Bfac: 76.14 4499 reflections ( 99.67 % complete ) and 0 restraints for refining 3658 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3514 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3669 (Rfree = 0.000) for 3658 atoms. Found 13 (23 requested) and removed 53 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 4.28 Search for helices and strands: 0 residues in 0 chains, 3738 seeds are put forward NCS extension: 0 residues added, 3738 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 6 peptides. Score 0.236 Round 2: 132 peptides, 24 chains. Longest chain 8 peptides. Score 0.352 Round 3: 144 peptides, 26 chains. Longest chain 9 peptides. Score 0.368 Round 4: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.382 Round 5: 143 peptides, 24 chains. Longest chain 14 peptides. Score 0.403 Taking the results from Round 5 Chains 24, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 7239 restraints for refining 2969 atoms. 6787 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3501 (Rfree = 0.000) for 2969 atoms. Found 5 (19 requested) and removed 42 (9 requested) atoms. Cycle 2: After refmac, R = 0.3449 (Rfree = 0.000) for 2880 atoms. Found 12 (18 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.3415 (Rfree = 0.000) for 2828 atoms. Found 8 (18 requested) and removed 27 (9 requested) atoms. Cycle 4: After refmac, R = 0.3402 (Rfree = 0.000) for 2789 atoms. Found 7 (18 requested) and removed 27 (9 requested) atoms. Cycle 5: After refmac, R = 0.3407 (Rfree = 0.000) for 2750 atoms. Found 8 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2892 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.227 Round 2: 117 peptides, 21 chains. Longest chain 9 peptides. Score 0.343 Round 3: 141 peptides, 27 chains. Longest chain 9 peptides. Score 0.335 Round 4: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.346 Round 5: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 24, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 5296 restraints for refining 2426 atoms. 4836 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3489 (Rfree = 0.000) for 2426 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 7: After refmac, R = 0.3417 (Rfree = 0.000) for 2384 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 8: After refmac, R = 0.3385 (Rfree = 0.000) for 2358 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.3281 (Rfree = 0.000) for 2344 atoms. Found 12 (15 requested) and removed 19 (7 requested) atoms. Cycle 10: After refmac, R = 0.3329 (Rfree = 0.000) for 2322 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 4.28 Search for helices and strands: 0 residues in 0 chains, 2435 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2446 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.330 Round 2: 133 peptides, 22 chains. Longest chain 11 peptides. Score 0.397 Round 3: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.431 Round 4: 145 peptides, 23 chains. Longest chain 11 peptides. Score 0.431 Round 5: 150 peptides, 23 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 5 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4971 restraints for refining 2360 atoms. 4486 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3527 (Rfree = 0.000) for 2360 atoms. Found 15 (15 requested) and removed 34 (7 requested) atoms. Cycle 12: After refmac, R = 0.3610 (Rfree = 0.000) for 2305 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 13: After refmac, R = 0.3589 (Rfree = 0.000) for 2285 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 14: After refmac, R = 0.3477 (Rfree = 0.000) for 2261 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.3496 (Rfree = 0.000) for 2249 atoms. Found 8 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2377 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 9 peptides. Score 0.255 Round 2: 133 peptides, 26 chains. Longest chain 11 peptides. Score 0.317 Round 3: 145 peptides, 26 chains. Longest chain 12 peptides. Score 0.373 Round 4: 149 peptides, 26 chains. Longest chain 14 peptides. Score 0.391 Round 5: 138 peptides, 22 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 22, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4737 restraints for refining 2214 atoms. 4295 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3747 (Rfree = 0.000) for 2214 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 17: After refmac, R = 0.3778 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 18: After refmac, R = 0.3604 (Rfree = 0.000) for 2167 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.3512 (Rfree = 0.000) for 2141 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 20: After refmac, R = 0.3516 (Rfree = 0.000) for 2126 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 4.34 Search for helices and strands: 0 residues in 0 chains, 2239 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2256 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 10 peptides. Score 0.267 Round 2: 132 peptides, 25 chains. Longest chain 10 peptides. Score 0.332 Round 3: 124 peptides, 23 chains. Longest chain 10 peptides. Score 0.335 Round 4: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.352 Round 5: 104 peptides, 15 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4588 restraints for refining 2155 atoms. 4219 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3621 (Rfree = 0.000) for 2155 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 22: After refmac, R = 0.3566 (Rfree = 0.000) for 2126 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.3484 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.3499 (Rfree = 0.000) for 2089 atoms. Found 12 (13 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.3593 (Rfree = 0.000) for 2080 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 4.28 Search for helices and strands: 0 residues in 0 chains, 2168 seeds are put forward NCS extension: 0 residues added, 2168 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 10 peptides. Score 0.275 Round 2: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.344 Round 3: 132 peptides, 23 chains. Longest chain 10 peptides. Score 0.372 Round 4: 136 peptides, 25 chains. Longest chain 13 peptides. Score 0.351 Round 5: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Chains 24, Residues 110, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4435 restraints for refining 2136 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3650 (Rfree = 0.000) for 2136 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.3652 (Rfree = 0.000) for 2105 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 28: After refmac, R = 0.3501 (Rfree = 0.000) for 2077 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.3462 (Rfree = 0.000) for 2067 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 30: After refmac, R = 0.3466 (Rfree = 0.000) for 2054 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2160 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2172 seeds are put forward Round 1: 105 peptides, 19 chains. Longest chain 11 peptides. Score 0.326 Round 2: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.379 Round 3: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.336 Round 4: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.377 Round 5: 111 peptides, 19 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 2 Chains 19, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4090 restraints for refining 2014 atoms. 3721 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3498 (Rfree = 0.000) for 2014 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 32: After refmac, R = 0.3468 (Rfree = 0.000) for 1994 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.3495 (Rfree = 0.000) for 1986 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 34: After refmac, R = 0.3471 (Rfree = 0.000) for 1975 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 35: After refmac, R = 0.3407 (Rfree = 0.000) for 1969 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2076 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.309 Round 2: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.369 Round 3: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.374 Round 4: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.407 Round 5: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 4 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 3975 restraints for refining 2018 atoms. 3634 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3543 (Rfree = 0.000) for 2018 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 37: After refmac, R = 0.3664 (Rfree = 0.000) for 1995 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.3437 (Rfree = 0.000) for 1980 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.3501 (Rfree = 0.000) for 1977 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.3407 (Rfree = 0.000) for 1954 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 2041 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2053 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.230 Round 2: 102 peptides, 20 chains. Longest chain 7 peptides. Score 0.289 Round 3: 109 peptides, 21 chains. Longest chain 11 peptides. Score 0.303 Round 4: 100 peptides, 18 chains. Longest chain 13 peptides. Score 0.323 Round 5: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.347 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4006 restraints for refining 2010 atoms. 3702 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3653 (Rfree = 0.000) for 2010 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 42: After refmac, R = 0.3727 (Rfree = 0.000) for 1969 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 43: After refmac, R = 0.3107 (Rfree = 0.000) for 1946 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.3147 (Rfree = 0.000) for 1935 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.3295 (Rfree = 0.000) for 1926 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 1987 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2001 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.225 Round 2: 109 peptides, 20 chains. Longest chain 9 peptides. Score 0.325 Round 3: 106 peptides, 19 chains. Longest chain 12 peptides. Score 0.331 Round 4: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.296 Round 5: 107 peptides, 19 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 88, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2itb-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (88 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4499 reflections ( 99.67 % complete ) and 4113 restraints for refining 2016 atoms. 3736 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3630 (Rfree = 0.000) for 2016 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3674 (Rfree = 0.000) for 1992 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3795 (Rfree = 0.000) for 1977 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3654 (Rfree = 0.000) for 1960 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Sun 23 Dec 23:05:49 GMT 2018 Job finished. TimeTaking 43.11