null Mon 24 Dec 07:59:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:59:15 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-parrot-noncs/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 355 and 0 Target number of residues in the AU: 355 Target solvent content: 0.6485 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.4-parrot-noncs.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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.400 Wilson plot Bfac: 76.83 7942 reflections ( 99.75 % complete ) and 0 restraints for refining 4437 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3226 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3029 (Rfree = 0.000) for 4437 atoms. Found 27 (33 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 4520 seeds are put forward NCS extension: 0 residues added, 4520 seeds are put forward Round 1: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.384 Round 2: 286 peptides, 35 chains. Longest chain 25 peptides. Score 0.598 Round 3: 301 peptides, 40 chains. Longest chain 16 peptides. Score 0.581 Round 4: 312 peptides, 36 chains. Longest chain 24 peptides. Score 0.643 Round 5: 304 peptides, 35 chains. Longest chain 25 peptides. Score 0.636 Taking the results from Round 4 Chains 38, Residues 276, Estimated correctness of the model 42.1 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7880 restraints for refining 3636 atoms. 6692 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2582 (Rfree = 0.000) for 3636 atoms. Found 16 (27 requested) and removed 25 (13 requested) atoms. Cycle 2: After refmac, R = 0.2385 (Rfree = 0.000) for 3592 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 3: After refmac, R = 0.2312 (Rfree = 0.000) for 3562 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 3543 atoms. Found 2 (26 requested) and removed 15 (13 requested) atoms. Cycle 5: After refmac, R = 0.2233 (Rfree = 0.000) for 3524 atoms. Found 7 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 3652 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3686 seeds are put forward Round 1: 263 peptides, 38 chains. Longest chain 22 peptides. Score 0.511 Round 2: 303 peptides, 39 chains. Longest chain 21 peptides. Score 0.595 Round 3: 292 peptides, 37 chains. Longest chain 16 peptides. Score 0.591 Round 4: 294 peptides, 38 chains. Longest chain 21 peptides. Score 0.585 Round 5: 296 peptides, 37 chains. Longest chain 17 peptides. Score 0.600 Taking the results from Round 5 Chains 38, Residues 259, Estimated correctness of the model 28.7 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8021 restraints for refining 3635 atoms. 6879 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2522 (Rfree = 0.000) for 3635 atoms. Found 16 (27 requested) and removed 31 (13 requested) atoms. Cycle 7: After refmac, R = 0.2425 (Rfree = 0.000) for 3606 atoms. Found 5 (27 requested) and removed 19 (13 requested) atoms. Cycle 8: After refmac, R = 0.2332 (Rfree = 0.000) for 3582 atoms. Found 9 (27 requested) and removed 16 (13 requested) atoms. Cycle 9: After refmac, R = 0.2187 (Rfree = 0.000) for 3568 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. Cycle 10: After refmac, R = 0.2164 (Rfree = 0.000) for 3557 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 3674 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3690 seeds are put forward Round 1: 268 peptides, 43 chains. Longest chain 16 peptides. Score 0.467 Round 2: 287 peptides, 40 chains. Longest chain 17 peptides. Score 0.549 Round 3: 298 peptides, 38 chains. Longest chain 17 peptides. Score 0.594 Round 4: 294 peptides, 38 chains. Longest chain 18 peptides. Score 0.585 Round 5: 287 peptides, 37 chains. Longest chain 17 peptides. Score 0.580 Taking the results from Round 3 Chains 38, Residues 260, Estimated correctness of the model 26.7 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8252 restraints for refining 3637 atoms. 7190 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2323 (Rfree = 0.000) for 3637 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 12: After refmac, R = 0.2173 (Rfree = 0.000) for 3612 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 13: After refmac, R = 0.2106 (Rfree = 0.000) for 3592 atoms. Found 4 (27 requested) and removed 16 (13 requested) atoms. Cycle 14: After refmac, R = 0.2086 (Rfree = 0.000) for 3574 atoms. Found 4 (27 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.1979 (Rfree = 0.000) for 3554 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3706 seeds are put forward Round 1: 251 peptides, 38 chains. Longest chain 13 peptides. Score 0.480 Round 2: 293 peptides, 35 chains. Longest chain 30 peptides. Score 0.613 Round 3: 287 peptides, 31 chains. Longest chain 26 peptides. Score 0.639 Round 4: 277 peptides, 31 chains. Longest chain 19 peptides. Score 0.618 Round 5: 305 peptides, 35 chains. Longest chain 19 peptides. Score 0.638 Taking the results from Round 3 Chains 31, Residues 256, Estimated correctness of the model 40.9 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8027 restraints for refining 3637 atoms. 6934 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2298 (Rfree = 0.000) for 3637 atoms. Found 17 (27 requested) and removed 25 (13 requested) atoms. Cycle 17: After refmac, R = 0.2335 (Rfree = 0.000) for 3605 atoms. Found 14 (27 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.2057 (Rfree = 0.000) for 3587 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2314 (Rfree = 0.000) for 3571 atoms. Found 21 (27 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.2015 (Rfree = 0.000) for 3570 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 3688 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 3710 seeds are put forward Round 1: 256 peptides, 44 chains. Longest chain 16 peptides. Score 0.422 Round 2: 289 peptides, 39 chains. Longest chain 17 peptides. Score 0.564 Round 3: 290 peptides, 36 chains. Longest chain 18 peptides. Score 0.597 Round 4: 292 peptides, 38 chains. Longest chain 18 peptides. Score 0.581 Round 5: 302 peptides, 35 chains. Longest chain 21 peptides. Score 0.632 Taking the results from Round 5 Chains 35, Residues 267, Estimated correctness of the model 38.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8255 restraints for refining 3636 atoms. 7222 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2263 (Rfree = 0.000) for 3636 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 22: After refmac, R = 0.2053 (Rfree = 0.000) for 3619 atoms. Found 7 (27 requested) and removed 13 (13 requested) atoms. Cycle 23: After refmac, R = 0.1974 (Rfree = 0.000) for 3610 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.1924 (Rfree = 0.000) for 3598 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.1903 (Rfree = 0.000) for 3588 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3715 seeds are put forward Round 1: 252 peptides, 41 chains. Longest chain 14 peptides. Score 0.447 Round 2: 284 peptides, 38 chains. Longest chain 17 peptides. Score 0.562 Round 3: 283 peptides, 33 chains. Longest chain 18 peptides. Score 0.611 Round 4: 289 peptides, 33 chains. Longest chain 21 peptides. Score 0.624 Round 5: 277 peptides, 31 chains. Longest chain 22 peptides. Score 0.618 Taking the results from Round 4 Chains 33, Residues 256, Estimated correctness of the model 36.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8284 restraints for refining 3637 atoms. 7293 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2163 (Rfree = 0.000) for 3637 atoms. Found 10 (27 requested) and removed 13 (13 requested) atoms. Cycle 27: After refmac, R = 0.2033 (Rfree = 0.000) for 3628 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 28: After refmac, R = 0.2191 (Rfree = 0.000) for 3611 atoms. Found 11 (27 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.1931 (Rfree = 0.000) for 3599 atoms. Found 8 (27 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2243 (Rfree = 0.000) for 3591 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3728 seeds are put forward Round 1: 233 peptides, 40 chains. Longest chain 14 peptides. Score 0.405 Round 2: 262 peptides, 35 chains. Longest chain 20 peptides. Score 0.542 Round 3: 247 peptides, 35 chains. Longest chain 25 peptides. Score 0.504 Round 4: 253 peptides, 38 chains. Longest chain 18 peptides. Score 0.485 Round 5: 267 peptides, 34 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 5 Chains 35, Residues 233, Estimated correctness of the model 16.8 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8145 restraints for refining 3636 atoms. 7130 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2123 (Rfree = 0.000) for 3636 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 3614 atoms. Found 5 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.1871 (Rfree = 0.000) for 3597 atoms. Found 6 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.1886 (Rfree = 0.000) for 3585 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.1847 (Rfree = 0.000) for 3568 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3697 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 3732 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 12 peptides. Score 0.397 Round 2: 257 peptides, 39 chains. Longest chain 16 peptides. Score 0.484 Round 3: 277 peptides, 40 chains. Longest chain 23 peptides. Score 0.524 Round 4: 246 peptides, 38 chains. Longest chain 19 peptides. Score 0.466 Round 5: 266 peptides, 39 chains. Longest chain 16 peptides. Score 0.508 Taking the results from Round 3 Chains 41, Residues 237, Estimated correctness of the model 1.9 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7928 restraints for refining 3637 atoms. 6899 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 3637 atoms. Found 16 (27 requested) and removed 15 (13 requested) atoms. Cycle 37: After refmac, R = 0.1977 (Rfree = 0.000) for 3628 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 38: After refmac, R = 0.1946 (Rfree = 0.000) for 3610 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 3596 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1967 (Rfree = 0.000) for 3583 atoms. Found 6 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3684 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3700 seeds are put forward Round 1: 200 peptides, 35 chains. Longest chain 12 peptides. Score 0.371 Round 2: 244 peptides, 37 chains. Longest chain 17 peptides. Score 0.473 Round 3: 239 peptides, 36 chains. Longest chain 18 peptides. Score 0.471 Round 4: 259 peptides, 37 chains. Longest chain 19 peptides. Score 0.512 Round 5: 246 peptides, 33 chains. Longest chain 17 peptides. Score 0.525 Taking the results from Round 5 Chains 33, Residues 213, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8605 restraints for refining 3637 atoms. 7786 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2106 (Rfree = 0.000) for 3637 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. Cycle 42: After refmac, R = 0.1999 (Rfree = 0.000) for 3634 atoms. Found 5 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.1924 (Rfree = 0.000) for 3623 atoms. Found 5 (27 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1886 (Rfree = 0.000) for 3614 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1853 (Rfree = 0.000) for 3602 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3735 seeds are put forward Round 1: 211 peptides, 41 chains. Longest chain 12 peptides. Score 0.326 Round 2: 230 peptides, 37 chains. Longest chain 16 peptides. Score 0.434 Round 3: 235 peptides, 39 chains. Longest chain 14 peptides. Score 0.424 Round 4: 251 peptides, 40 chains. Longest chain 18 peptides. Score 0.456 Round 5: 256 peptides, 36 chains. Longest chain 18 peptides. Score 0.516 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 220, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7942 reflections ( 99.75 % complete ) and 8458 restraints for refining 3637 atoms. 7597 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2162 (Rfree = 0.000) for 3637 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 3621 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2057 (Rfree = 0.000) for 3606 atoms. Found 0 (27 requested) and removed 7 (13 requested) atoms. Cycle 49: After refmac, R = 0.2019 (Rfree = 0.000) for 3596 atoms. Found 0 (27 requested) and removed 3 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:49:34 GMT 2018 Job finished. TimeTaking 50.4 Used memory is bytes: 9003448