Mon 24 Dec 00:17:11 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ogi-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-mrncs ############### 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 00:17:16 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-mrncs/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 281 and 0 Target number of residues in the AU: 281 Target solvent content: 0.6557 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-3.6-parrot-mrncs.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: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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: 63.833 3.600 Wilson plot Bfac: 81.58 5214 reflections ( 99.79 % complete ) and 0 restraints for refining 3464 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3474 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3158 (Rfree = 0.000) for 3464 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 3548 seeds are put forward NCS extension: 0 residues added, 3548 seeds are put forward Round 1: 152 peptides, 32 chains. Longest chain 8 peptides. Score 0.271 Round 2: 191 peptides, 29 chains. Longest chain 21 peptides. Score 0.465 Round 3: 200 peptides, 35 chains. Longest chain 10 peptides. Score 0.406 Round 4: 218 peptides, 30 chains. Longest chain 19 peptides. Score 0.537 Round 5: 218 peptides, 31 chains. Longest chain 18 peptides. Score 0.524 Taking the results from Round 4 Chains 32, Residues 188, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6239 restraints for refining 2843 atoms. 5446 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2539 (Rfree = 0.000) for 2843 atoms. Found 12 (18 requested) and removed 27 (9 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 2789 atoms. Found 12 (18 requested) and removed 29 (9 requested) atoms. Cycle 3: After refmac, R = 0.2281 (Rfree = 0.000) for 2744 atoms. Found 13 (17 requested) and removed 21 (8 requested) atoms. Cycle 4: After refmac, R = 0.2209 (Rfree = 0.000) for 2717 atoms. Found 16 (17 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.2141 (Rfree = 0.000) for 2702 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 2854 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2876 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 18 peptides. Score 0.400 Round 2: 224 peptides, 34 chains. Longest chain 15 peptides. Score 0.501 Round 3: 237 peptides, 36 chains. Longest chain 18 peptides. Score 0.515 Round 4: 232 peptides, 33 chains. Longest chain 16 peptides. Score 0.539 Round 5: 220 peptides, 32 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 4 Chains 33, Residues 199, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6353 restraints for refining 2840 atoms. 5569 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2247 (Rfree = 0.000) for 2840 atoms. Found 12 (18 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 2801 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 2786 atoms. Found 11 (17 requested) and removed 21 (8 requested) atoms. Cycle 9: After refmac, R = 0.1982 (Rfree = 0.000) for 2764 atoms. Found 12 (17 requested) and removed 23 (8 requested) atoms. Cycle 10: After refmac, R = 0.1866 (Rfree = 0.000) for 2743 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 2895 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2914 seeds are put forward Round 1: 193 peptides, 36 chains. Longest chain 9 peptides. Score 0.365 Round 2: 223 peptides, 34 chains. Longest chain 14 peptides. Score 0.498 Round 3: 225 peptides, 34 chains. Longest chain 15 peptides. Score 0.505 Round 4: 235 peptides, 33 chains. Longest chain 15 peptides. Score 0.548 Round 5: 228 peptides, 31 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 5 Chains 32, Residues 197, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6118 restraints for refining 2843 atoms. 5303 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2153 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 12: After refmac, R = 0.2055 (Rfree = 0.000) for 2817 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 13: After refmac, R = 0.1941 (Rfree = 0.000) for 2806 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.2014 (Rfree = 0.000) for 2794 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1638 (Rfree = 0.000) for 2794 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2946 seeds are put forward Round 1: 198 peptides, 33 chains. Longest chain 12 peptides. Score 0.429 Round 2: 211 peptides, 29 chains. Longest chain 19 peptides. Score 0.530 Round 3: 224 peptides, 33 chains. Longest chain 14 peptides. Score 0.515 Round 4: 218 peptides, 27 chains. Longest chain 21 peptides. Score 0.577 Round 5: 235 peptides, 33 chains. Longest chain 14 peptides. Score 0.548 Taking the results from Round 4 Chains 27, Residues 191, Estimated correctness of the model 5.5 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6192 restraints for refining 2841 atoms. 5377 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2240 (Rfree = 0.000) for 2841 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 17: After refmac, R = 0.2132 (Rfree = 0.000) for 2812 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 18: After refmac, R = 0.2093 (Rfree = 0.000) for 2807 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2071 (Rfree = 0.000) for 2801 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1950 (Rfree = 0.000) for 2802 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2954 seeds are put forward Round 1: 193 peptides, 33 chains. Longest chain 12 peptides. Score 0.412 Round 2: 213 peptides, 29 chains. Longest chain 18 peptides. Score 0.536 Round 3: 214 peptides, 31 chains. Longest chain 19 peptides. Score 0.511 Round 4: 201 peptides, 27 chains. Longest chain 20 peptides. Score 0.526 Round 5: 209 peptides, 27 chains. Longest chain 16 peptides. Score 0.551 Taking the results from Round 5 Chains 28, Residues 182, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6331 restraints for refining 2842 atoms. 5606 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2095 (Rfree = 0.000) for 2842 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 22: After refmac, R = 0.2131 (Rfree = 0.000) for 2829 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.1900 (Rfree = 0.000) for 2826 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1971 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 25: After refmac, R = 0.1805 (Rfree = 0.000) for 2827 atoms. Found 14 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 2956 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2976 seeds are put forward Round 1: 170 peptides, 29 chains. Longest chain 14 peptides. Score 0.391 Round 2: 187 peptides, 29 chains. Longest chain 13 peptides. Score 0.452 Round 3: 179 peptides, 27 chains. Longest chain 14 peptides. Score 0.454 Round 4: 191 peptides, 28 chains. Longest chain 19 peptides. Score 0.480 Round 5: 191 peptides, 28 chains. Longest chain 19 peptides. Score 0.480 Taking the results from Round 5 Chains 29, Residues 163, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6365 restraints for refining 2842 atoms. 5685 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2268 (Rfree = 0.000) for 2842 atoms. Found 17 (18 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2078 (Rfree = 0.000) for 2820 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 28: After refmac, R = 0.1962 (Rfree = 0.000) for 2813 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. Cycle 29: After refmac, R = 0.1921 (Rfree = 0.000) for 2803 atoms. Found 14 (18 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.1586 (Rfree = 0.000) for 2798 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 0 residues added, 2920 seeds are put forward Round 1: 151 peptides, 28 chains. Longest chain 11 peptides. Score 0.335 Round 2: 163 peptides, 28 chains. Longest chain 12 peptides. Score 0.381 Round 3: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.401 Round 4: 171 peptides, 26 chains. Longest chain 15 peptides. Score 0.442 Round 5: 170 peptides, 29 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 4 Chains 26, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6667 restraints for refining 2828 atoms. 6113 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2084 (Rfree = 0.000) for 2828 atoms. Found 15 (18 requested) and removed 27 (9 requested) atoms. Cycle 32: After refmac, R = 0.1987 (Rfree = 0.000) for 2806 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 33: After refmac, R = 0.1955 (Rfree = 0.000) for 2803 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.1964 (Rfree = 0.000) for 2803 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.1849 (Rfree = 0.000) for 2804 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 2965 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 15 peptides. Score 0.344 Round 2: 154 peptides, 25 chains. Longest chain 15 peptides. Score 0.396 Round 3: 160 peptides, 26 chains. Longest chain 15 peptides. Score 0.402 Round 4: 165 peptides, 25 chains. Longest chain 15 peptides. Score 0.436 Round 5: 157 peptides, 28 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Chains 25, Residues 140, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6516 restraints for refining 2827 atoms. 5970 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2043 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 37: After refmac, R = 0.1940 (Rfree = 0.000) for 2820 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.1854 (Rfree = 0.000) for 2822 atoms. Found 17 (18 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.1943 (Rfree = 0.000) for 2825 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 40: After refmac, R = 0.1849 (Rfree = 0.000) for 2826 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 0 residues added, 2957 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 8 peptides. Score 0.269 Round 2: 155 peptides, 28 chains. Longest chain 15 peptides. Score 0.350 Round 3: 146 peptides, 25 chains. Longest chain 9 peptides. Score 0.366 Round 4: 163 peptides, 28 chains. Longest chain 15 peptides. Score 0.381 Round 5: 172 peptides, 27 chains. Longest chain 18 peptides. Score 0.430 Taking the results from Round 5 Chains 27, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6574 restraints for refining 2843 atoms. 6021 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2149 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2016 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.1979 (Rfree = 0.000) for 2837 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.1913 (Rfree = 0.000) for 2839 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.1542 (Rfree = 0.000) for 2839 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2974 seeds are put forward Round 1: 118 peptides, 26 chains. Longest chain 7 peptides. Score 0.232 Round 2: 151 peptides, 28 chains. Longest chain 9 peptides. Score 0.335 Round 3: 159 peptides, 25 chains. Longest chain 14 peptides. Score 0.415 Round 4: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.382 Round 5: 151 peptides, 24 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 134, 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 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5214 reflections ( 99.79 % complete ) and 6566 restraints for refining 2842 atoms. 6055 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1845 (Rfree = 0.000) for 2842 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1910 (Rfree = 0.000) for 2829 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1792 (Rfree = 0.000) for 2817 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1852 (Rfree = 0.000) for 2806 atoms. TimeTaking 34.55