Mon 24 Dec 07:52:27 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 2owp-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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/2owp-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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 07:52:31 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/2owp-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6393 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.8-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.15 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: 29.899 3.802 Wilson plot Bfac: 71.04 4543 reflections ( 99.15 % complete ) and 0 restraints for refining 2281 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3812 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3721 (Rfree = 0.000) for 2281 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 2.78 Search for helices and strands: 0 residues in 0 chains, 2315 seeds are put forward NCS extension: 0 residues added, 2315 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 8 peptides. Score 0.243 Round 2: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.373 Round 3: 140 peptides, 21 chains. Longest chain 17 peptides. Score 0.413 Round 4: 150 peptides, 23 chains. Longest chain 14 peptides. Score 0.417 Round 5: 147 peptides, 21 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 5 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4155 restraints for refining 1867 atoms. 3672 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3878 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.3829 (Rfree = 0.000) for 1823 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 3: After refmac, R = 0.3628 (Rfree = 0.000) for 1784 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.3415 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.3555 (Rfree = 0.000) for 1739 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 2.72 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1814 seeds are put forward Round 1: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.371 Round 2: 162 peptides, 20 chains. Longest chain 15 peptides. Score 0.507 Round 3: 161 peptides, 24 chains. Longest chain 13 peptides. Score 0.441 Round 4: 160 peptides, 22 chains. Longest chain 16 peptides. Score 0.469 Round 5: 164 peptides, 22 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 2 Chains 20, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3725 restraints for refining 1792 atoms. 3177 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3690 (Rfree = 0.000) for 1792 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 7: After refmac, R = 0.3538 (Rfree = 0.000) for 1751 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.3710 (Rfree = 0.000) for 1725 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.3637 (Rfree = 0.000) for 1702 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.3699 (Rfree = 0.000) for 1683 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 2.65 Search for helices and strands: 0 residues in 0 chains, 1746 seeds are put forward NCS extension: 0 residues added, 1746 seeds are put forward Round 1: 139 peptides, 27 chains. Longest chain 9 peptides. Score 0.305 Round 2: 165 peptides, 24 chains. Longest chain 17 peptides. Score 0.455 Round 3: 165 peptides, 22 chains. Longest chain 14 peptides. Score 0.486 Round 4: 162 peptides, 20 chains. Longest chain 16 peptides. Score 0.507 Round 5: 162 peptides, 19 chains. Longest chain 21 peptides. Score 0.522 Taking the results from Round 5 Chains 19, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3984 restraints for refining 1867 atoms. 3431 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3888 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.3883 (Rfree = 0.000) for 1830 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 13: After refmac, R = 0.3780 (Rfree = 0.000) for 1803 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.3688 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.3724 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 0 residues added, 1821 seeds are put forward Round 1: 148 peptides, 28 chains. Longest chain 9 peptides. Score 0.324 Round 2: 155 peptides, 24 chains. Longest chain 17 peptides. Score 0.419 Round 3: 137 peptides, 19 chains. Longest chain 15 peptides. Score 0.436 Round 4: 142 peptides, 21 chains. Longest chain 19 peptides. Score 0.421 Round 5: 159 peptides, 24 chains. Longest chain 15 peptides. Score 0.434 Taking the results from Round 3 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4229 restraints for refining 1867 atoms. 3776 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3865 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 17: After refmac, R = 0.3868 (Rfree = 0.000) for 1840 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 18: After refmac, R = 0.3770 (Rfree = 0.000) for 1818 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 19: After refmac, R = 0.3748 (Rfree = 0.000) for 1800 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 20: After refmac, R = 0.3623 (Rfree = 0.000) for 1781 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 2.65 Search for helices and strands: 0 residues in 0 chains, 1846 seeds are put forward NCS extension: 0 residues added, 1846 seeds are put forward Round 1: 145 peptides, 26 chains. Longest chain 12 peptides. Score 0.347 Round 2: 148 peptides, 24 chains. Longest chain 16 peptides. Score 0.393 Round 3: 137 peptides, 22 chains. Longest chain 17 peptides. Score 0.385 Round 4: 149 peptides, 24 chains. Longest chain 12 peptides. Score 0.397 Round 5: 157 peptides, 26 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 4 Chains 24, Residues 125, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4050 restraints for refining 1867 atoms. 3537 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3736 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 22: After refmac, R = 0.3290 (Rfree = 0.000) for 1820 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 23: After refmac, R = 0.3130 (Rfree = 0.000) for 1803 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.3134 (Rfree = 0.000) for 1801 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.3040 (Rfree = 0.000) for 1802 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.58 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1870 seeds are put forward Round 1: 121 peptides, 20 chains. Longest chain 9 peptides. Score 0.356 Round 2: 136 peptides, 22 chains. Longest chain 15 peptides. Score 0.381 Round 3: 144 peptides, 23 chains. Longest chain 12 peptides. Score 0.394 Round 4: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.379 Round 5: 129 peptides, 22 chains. Longest chain 14 peptides. Score 0.353 Taking the results from Round 3 Chains 23, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4024 restraints for refining 1867 atoms. 3563 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3200 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.3136 (Rfree = 0.000) for 1848 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.3038 (Rfree = 0.000) for 1846 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2976 (Rfree = 0.000) for 1835 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2967 (Rfree = 0.000) for 1830 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1885 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1897 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 18 peptides. Score 0.363 Round 2: 154 peptides, 23 chains. Longest chain 15 peptides. Score 0.432 Round 3: 145 peptides, 24 chains. Longest chain 11 peptides. Score 0.381 Round 4: 152 peptides, 25 chains. Longest chain 11 peptides. Score 0.391 Round 5: 143 peptides, 22 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 2 Chains 23, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4150 restraints for refining 1867 atoms. 3649 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3437 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.3597 (Rfree = 0.000) for 1850 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.3561 (Rfree = 0.000) for 1826 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 34: After refmac, R = 0.3800 (Rfree = 0.000) for 1816 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 35: After refmac, R = 0.3625 (Rfree = 0.000) for 1792 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1875 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.301 Round 2: 139 peptides, 23 chains. Longest chain 14 peptides. Score 0.375 Round 3: 146 peptides, 23 chains. Longest chain 11 peptides. Score 0.402 Round 4: 142 peptides, 23 chains. Longest chain 16 peptides. Score 0.387 Round 5: 152 peptides, 23 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 5 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4099 restraints for refining 1866 atoms. 3606 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3812 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 37: After refmac, R = 0.3676 (Rfree = 0.000) for 1827 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.3742 (Rfree = 0.000) for 1808 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 39: After refmac, R = 0.3616 (Rfree = 0.000) for 1790 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 40: After refmac, R = 0.3618 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 2.54 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 0 residues added, 1830 seeds are put forward Round 1: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.320 Round 2: 154 peptides, 27 chains. Longest chain 9 peptides. Score 0.365 Round 3: 153 peptides, 24 chains. Longest chain 11 peptides. Score 0.412 Round 4: 154 peptides, 23 chains. Longest chain 14 peptides. Score 0.432 Round 5: 143 peptides, 24 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 4 Chains 24, Residues 131, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3877 restraints for refining 1867 atoms. 3347 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3871 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 42: After refmac, R = 0.3737 (Rfree = 0.000) for 1826 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.3711 (Rfree = 0.000) for 1802 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.3673 (Rfree = 0.000) for 1785 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 45: After refmac, R = 0.3741 (Rfree = 0.000) for 1757 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1797 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.269 Round 2: 131 peptides, 22 chains. Longest chain 9 peptides. Score 0.361 Round 3: 133 peptides, 21 chains. Longest chain 14 peptides. Score 0.386 Round 4: 138 peptides, 23 chains. Longest chain 13 peptides. Score 0.371 Round 5: 134 peptides, 23 chains. Longest chain 13 peptides. Score 0.355 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2owp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4543 reflections ( 99.15 % complete ) and 4117 restraints for refining 1867 atoms. 3690 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3830 (Rfree = 0.000) for 1867 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3848 (Rfree = 0.000) for 1846 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3777 (Rfree = 0.000) for 1823 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3657 (Rfree = 0.000) for 1803 atoms. TimeTaking 28.4