Sun 23 Dec 22:22:56 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 1z82-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-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/1z82-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-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 22:23:05 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/1z82-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.2-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 420 and 0 Target number of residues in the AU: 420 Target solvent content: 0.6268 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.2-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 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 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: 29.850 3.200 Wilson plot Bfac: 64.58 10035 reflections ( 99.62 % complete ) and 0 restraints for refining 5998 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3009 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2229 (Rfree = 0.000) for 5998 atoms. Found 16 (53 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 6098 seeds are put forward NCS extension: 0 residues added, 6098 seeds are put forward Round 1: 302 peptides, 59 chains. Longest chain 12 peptides. Score 0.356 Round 2: 380 peptides, 57 chains. Longest chain 24 peptides. Score 0.561 Round 3: 390 peptides, 52 chains. Longest chain 25 peptides. Score 0.622 Round 4: 432 peptides, 55 chains. Longest chain 23 peptides. Score 0.672 Round 5: 436 peptides, 54 chains. Longest chain 28 peptides. Score 0.685 Taking the results from Round 5 Chains 54, Residues 382, Estimated correctness of the model 61.9 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10337 restraints for refining 4892 atoms. 8681 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 4892 atoms. Found 35 (43 requested) and removed 43 (21 requested) atoms. Cycle 2: After refmac, R = 0.2272 (Rfree = 0.000) for 4830 atoms. Found 18 (43 requested) and removed 33 (21 requested) atoms. Cycle 3: After refmac, R = 0.2388 (Rfree = 0.000) for 4768 atoms. Found 27 (43 requested) and removed 36 (21 requested) atoms. Cycle 4: After refmac, R = 0.2278 (Rfree = 0.000) for 4734 atoms. Found 23 (42 requested) and removed 31 (21 requested) atoms. Cycle 5: After refmac, R = 0.2127 (Rfree = 0.000) for 4708 atoms. Found 13 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4886 seeds are put forward NCS extension: 42 residues added (15 deleted due to clashes), 4928 seeds are put forward Round 1: 379 peptides, 60 chains. Longest chain 18 peptides. Score 0.531 Round 2: 422 peptides, 57 chains. Longest chain 25 peptides. Score 0.640 Round 3: 430 peptides, 50 chains. Longest chain 33 peptides. Score 0.703 Round 4: 422 peptides, 49 chains. Longest chain 23 peptides. Score 0.698 Round 5: 429 peptides, 47 chains. Longest chain 21 peptides. Score 0.722 Taking the results from Round 5 Chains 51, Residues 382, Estimated correctness of the model 69.7 % 6 chains (60 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 B and 150 B 49 chains (386 residues) following loop building 5 chains (66 residues) in sequence following loop building ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 9822 restraints for refining 4741 atoms. 8117 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2700 (Rfree = 0.000) for 4741 atoms. Found 42 (42 requested) and removed 39 (21 requested) atoms. Cycle 7: After refmac, R = 0.2411 (Rfree = 0.000) for 4739 atoms. Found 20 (41 requested) and removed 25 (21 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 4721 atoms. Found 5 (40 requested) and removed 22 (21 requested) atoms. Cycle 9: After refmac, R = 0.2158 (Rfree = 0.000) for 4691 atoms. Found 11 (39 requested) and removed 21 (21 requested) atoms. Cycle 10: After refmac, R = 0.2117 (Rfree = 0.000) for 4679 atoms. Found 4 (39 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 4821 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4842 seeds are put forward Round 1: 351 peptides, 53 chains. Longest chain 15 peptides. Score 0.536 Round 2: 409 peptides, 53 chains. Longest chain 23 peptides. Score 0.648 Round 3: 417 peptides, 52 chains. Longest chain 22 peptides. Score 0.669 Round 4: 423 peptides, 50 chains. Longest chain 28 peptides. Score 0.693 Round 5: 416 peptides, 56 chains. Longest chain 20 peptides. Score 0.637 Taking the results from Round 4 Chains 53, Residues 373, Estimated correctness of the model 63.7 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10337 restraints for refining 4819 atoms. 8687 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2611 (Rfree = 0.000) for 4819 atoms. Found 33 (39 requested) and removed 46 (21 requested) atoms. Cycle 12: After refmac, R = 0.2133 (Rfree = 0.000) for 4801 atoms. Found 14 (39 requested) and removed 23 (21 requested) atoms. Cycle 13: After refmac, R = 0.2060 (Rfree = 0.000) for 4774 atoms. Found 12 (39 requested) and removed 22 (21 requested) atoms. Cycle 14: After refmac, R = 0.1999 (Rfree = 0.000) for 4756 atoms. Found 8 (38 requested) and removed 24 (21 requested) atoms. Cycle 15: After refmac, R = 0.1932 (Rfree = 0.000) for 4732 atoms. Found 7 (38 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 4870 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 4897 seeds are put forward Round 1: 369 peptides, 59 chains. Longest chain 17 peptides. Score 0.519 Round 2: 399 peptides, 52 chains. Longest chain 20 peptides. Score 0.639 Round 3: 414 peptides, 48 chains. Longest chain 30 peptides. Score 0.693 Round 4: 404 peptides, 46 chains. Longest chain 22 peptides. Score 0.692 Round 5: 402 peptides, 50 chains. Longest chain 23 peptides. Score 0.659 Taking the results from Round 3 Chains 49, Residues 366, Estimated correctness of the model 63.7 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10392 restraints for refining 4800 atoms. 8833 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2402 (Rfree = 0.000) for 4800 atoms. Found 32 (39 requested) and removed 34 (21 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 4794 atoms. Found 11 (39 requested) and removed 22 (21 requested) atoms. Cycle 18: After refmac, R = 0.2048 (Rfree = 0.000) for 4780 atoms. Found 5 (38 requested) and removed 21 (21 requested) atoms. Cycle 19: After refmac, R = 0.1977 (Rfree = 0.000) for 4759 atoms. Found 15 (38 requested) and removed 21 (21 requested) atoms. Cycle 20: After refmac, R = 0.1979 (Rfree = 0.000) for 4748 atoms. Found 6 (38 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 4889 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 4917 seeds are put forward Round 1: 334 peptides, 50 chains. Longest chain 19 peptides. Score 0.528 Round 2: 393 peptides, 51 chains. Longest chain 23 peptides. Score 0.636 Round 3: 379 peptides, 50 chains. Longest chain 30 peptides. Score 0.619 Round 4: 386 peptides, 50 chains. Longest chain 20 peptides. Score 0.631 Round 5: 386 peptides, 45 chains. Longest chain 28 peptides. Score 0.670 Taking the results from Round 5 Chains 50, Residues 341, Estimated correctness of the model 58.5 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 10791 restraints for refining 4824 atoms. 9358 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2496 (Rfree = 0.000) for 4824 atoms. Found 39 (39 requested) and removed 34 (21 requested) atoms. Cycle 22: After refmac, R = 0.2178 (Rfree = 0.000) for 4827 atoms. Found 11 (39 requested) and removed 21 (21 requested) atoms. Cycle 23: After refmac, R = 0.1972 (Rfree = 0.000) for 4812 atoms. Found 11 (39 requested) and removed 21 (21 requested) atoms. Cycle 24: After refmac, R = 0.1975 (Rfree = 0.000) for 4798 atoms. Found 8 (39 requested) and removed 22 (21 requested) atoms. Cycle 25: After refmac, R = 0.1949 (Rfree = 0.000) for 4778 atoms. Found 17 (38 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4947 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 4963 seeds are put forward Round 1: 346 peptides, 59 chains. Longest chain 16 peptides. Score 0.466 Round 2: 398 peptides, 56 chains. Longest chain 21 peptides. Score 0.605 Round 3: 384 peptides, 54 chains. Longest chain 19 peptides. Score 0.595 Round 4: 386 peptides, 46 chains. Longest chain 20 peptides. Score 0.663 Round 5: 373 peptides, 52 chains. Longest chain 19 peptides. Score 0.590 Taking the results from Round 4 Chains 46, Residues 340, Estimated correctness of the model 56.9 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10035 reflections ( 99.62 % complete ) and 10794 restraints for refining 4877 atoms. 9344 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2162 (Rfree = 0.000) for 4877 atoms. Found 23 (39 requested) and removed 32 (21 requested) atoms. Cycle 27: After refmac, R = 0.2027 (Rfree = 0.000) for 4865 atoms. Found 9 (39 requested) and removed 23 (21 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2011 (Rfree = 0.000) for 4847 atoms. Found 9 (39 requested) and removed 21 (21 requested) atoms. Cycle 29: After refmac, R = 0.2033 (Rfree = 0.000) for 4832 atoms. Found 16 (39 requested) and removed 22 (21 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 4820 atoms. Found 17 (39 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 4948 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 4983 seeds are put forward Round 1: 311 peptides, 51 chains. Longest chain 15 peptides. Score 0.465 Round 2: 369 peptides, 50 chains. Longest chain 22 peptides. Score 0.600 Round 3: 363 peptides, 49 chains. Longest chain 19 peptides. Score 0.597 Round 4: 369 peptides, 48 chains. Longest chain 22 peptides. Score 0.617 Round 5: 369 peptides, 51 chains. Longest chain 22 peptides. Score 0.591 Taking the results from Round 4 Chains 48, Residues 321, Estimated correctness of the model 45.6 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 11160 restraints for refining 4894 atoms. 9853 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2292 (Rfree = 0.000) for 4894 atoms. Found 35 (39 requested) and removed 29 (21 requested) atoms. Cycle 32: After refmac, R = 0.2045 (Rfree = 0.000) for 4897 atoms. Found 15 (39 requested) and removed 24 (21 requested) atoms. Cycle 33: After refmac, R = 0.1934 (Rfree = 0.000) for 4885 atoms. Found 5 (39 requested) and removed 21 (21 requested) atoms. Cycle 34: After refmac, R = 0.1881 (Rfree = 0.000) for 4867 atoms. Found 2 (39 requested) and removed 21 (21 requested) atoms. Cycle 35: After refmac, R = 0.1865 (Rfree = 0.000) for 4845 atoms. Found 7 (39 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4977 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4997 seeds are put forward Round 1: 290 peptides, 52 chains. Longest chain 14 peptides. Score 0.402 Round 2: 349 peptides, 52 chains. Longest chain 19 peptides. Score 0.541 Round 3: 341 peptides, 54 chains. Longest chain 14 peptides. Score 0.504 Round 4: 342 peptides, 48 chains. Longest chain 16 peptides. Score 0.563 Round 5: 347 peptides, 51 chains. Longest chain 15 peptides. Score 0.546 Taking the results from Round 4 Chains 48, Residues 294, Estimated correctness of the model 30.7 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 11493 restraints for refining 4894 atoms. 10336 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2218 (Rfree = 0.000) for 4894 atoms. Found 33 (39 requested) and removed 24 (21 requested) atoms. Cycle 37: After refmac, R = 0.2011 (Rfree = 0.000) for 4902 atoms. Found 15 (40 requested) and removed 24 (22 requested) atoms. Cycle 38: After refmac, R = 0.1923 (Rfree = 0.000) for 4885 atoms. Found 17 (39 requested) and removed 22 (21 requested) atoms. Cycle 39: After refmac, R = 0.1999 (Rfree = 0.000) for 4875 atoms. Found 16 (39 requested) and removed 22 (21 requested) atoms. Cycle 40: After refmac, R = 0.1895 (Rfree = 0.000) for 4861 atoms. Found 12 (39 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 5029 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5046 seeds are put forward Round 1: 287 peptides, 56 chains. Longest chain 11 peptides. Score 0.349 Round 2: 335 peptides, 53 chains. Longest chain 13 peptides. Score 0.501 Round 3: 334 peptides, 51 chains. Longest chain 18 peptides. Score 0.518 Round 4: 340 peptides, 52 chains. Longest chain 16 peptides. Score 0.522 Round 5: 331 peptides, 51 chains. Longest chain 15 peptides. Score 0.511 Taking the results from Round 4 Chains 52, Residues 288, Estimated correctness of the model 18.3 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10035 reflections ( 99.62 % complete ) and 11356 restraints for refining 4894 atoms. 10225 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2254 (Rfree = 0.000) for 4894 atoms. Found 39 (39 requested) and removed 27 (21 requested) atoms. Cycle 42: After refmac, R = 0.2017 (Rfree = 0.000) for 4901 atoms. Found 14 (40 requested) and removed 22 (22 requested) atoms. Cycle 43: After refmac, R = 0.1903 (Rfree = 0.000) for 4891 atoms. Found 4 (39 requested) and removed 22 (21 requested) atoms. Cycle 44: After refmac, R = 0.1874 (Rfree = 0.000) for 4865 atoms. Found 10 (39 requested) and removed 21 (21 requested) atoms. Cycle 45: After refmac, R = 0.1810 (Rfree = 0.000) for 4850 atoms. Found 11 (39 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 4995 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5015 seeds are put forward Round 1: 257 peptides, 48 chains. Longest chain 17 peptides. Score 0.359 Round 2: 298 peptides, 46 chains. Longest chain 18 peptides. Score 0.485 Round 3: 283 peptides, 44 chains. Longest chain 18 peptides. Score 0.470 Round 4: 295 peptides, 48 chains. Longest chain 17 peptides. Score 0.457 Round 5: 290 peptides, 48 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 252, Estimated correctness of the model 6.4 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (252 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10035 reflections ( 99.62 % complete ) and 11465 restraints for refining 4871 atoms. 10460 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1991 (Rfree = 0.000) for 4871 atoms. Found 0 (39 requested) and removed 17 (21 requested) atoms. Cycle 47: After refmac, R = 0.1922 (Rfree = 0.000) for 4851 atoms. Found 0 (39 requested) and removed 7 (21 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1910 (Rfree = 0.000) for 4841 atoms. Found 0 (39 requested) and removed 0 (21 requested) atoms. Cycle 49: After refmac, R = 0.1887 (Rfree = 0.000) for 4839 atoms. TimeTaking 70.47