null Sun 23 Dec 22:22:46 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 2ozg-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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/2ozg-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 22:22:56 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/2ozg-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 300 and 0 Target number of residues in the AU: 300 Target solvent content: 0.6171 Checking the provided sequence file Detected sequence length: 396 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 396 Adjusted target solvent content: 0.49 Input MTZ file: 2ozg-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: 155 Cell parameters: 175.031 175.031 71.923 90.000 90.000 120.000 Input sequence file: 2ozg-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3168 target number of atoms Had to go as low as 0.70 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.516 3.200 Wilson plot Bfac: 59.90 7062 reflections ( 99.80 % complete ) and 0 restraints for refining 3511 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3108 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1990 (Rfree = 0.000) for 3511 atoms. Found 19 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.13 Search for helices and strands: 0 residues in 0 chains, 3608 seeds are put forward Round 1: 221 peptides, 38 chains. Longest chain 11 peptides. Score 0.443 Round 2: 242 peptides, 33 chains. Longest chain 19 peptides. Score 0.580 Round 3: 265 peptides, 27 chains. Longest chain 43 peptides. Score 0.707 Round 4: 267 peptides, 25 chains. Longest chain 60 peptides. Score 0.731 Round 5: 271 peptides, 29 chains. Longest chain 21 peptides. Score 0.700 Taking the results from Round 4 Chains 25, Residues 242, Estimated correctness of the model 71.5 % 2 chains (82 residues) have been docked in sequence Building loops using Loopy2018 25 chains (242 residues) following loop building 2 chains (82 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5478 restraints for refining 2954 atoms. 4192 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2530 (Rfree = 0.000) for 2954 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 2: After refmac, R = 0.2256 (Rfree = 0.000) for 2935 atoms. Found 9 (25 requested) and removed 16 (13 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 2906 atoms. Found 4 (25 requested) and removed 13 (13 requested) atoms. Cycle 4: After refmac, R = 0.2122 (Rfree = 0.000) for 2892 atoms. Found 4 (23 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.2094 (Rfree = 0.000) for 2877 atoms. Found 7 (23 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward Round 1: 273 peptides, 31 chains. Longest chain 44 peptides. Score 0.684 Round 2: 282 peptides, 28 chains. Longest chain 47 peptides. Score 0.732 Round 3: 290 peptides, 24 chains. Longest chain 50 peptides. Score 0.782 Round 4: 277 peptides, 27 chains. Longest chain 32 peptides. Score 0.732 Round 5: 277 peptides, 31 chains. Longest chain 29 peptides. Score 0.693 Taking the results from Round 3 Chains 26, Residues 266, Estimated correctness of the model 80.6 % 5 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 171 A and 178 A 24 chains (271 residues) following loop building 4 chains (103 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5095 restraints for refining 2890 atoms. 3622 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2572 (Rfree = 0.000) for 2890 atoms. Found 21 (22 requested) and removed 26 (12 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 2881 atoms. Found 11 (22 requested) and removed 12 (12 requested) atoms. Cycle 8: After refmac, R = 0.2153 (Rfree = 0.000) for 2877 atoms. Found 6 (21 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2110 (Rfree = 0.000) for 2864 atoms. Found 4 (21 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2091 (Rfree = 0.000) for 2855 atoms. Found 3 (20 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward Round 1: 260 peptides, 28 chains. Longest chain 41 peptides. Score 0.685 Round 2: 280 peptides, 24 chains. Longest chain 44 peptides. Score 0.765 Round 3: 289 peptides, 25 chains. Longest chain 54 peptides. Score 0.772 Round 4: 279 peptides, 27 chains. Longest chain 54 peptides. Score 0.736 Round 5: 272 peptides, 27 chains. Longest chain 34 peptides. Score 0.722 Taking the results from Round 3 Chains 28, Residues 264, Estimated correctness of the model 78.9 % 5 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 81 A Built loop between residues 87 A and 94 A 26 chains (276 residues) following loop building 3 chains (100 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5184 restraints for refining 2892 atoms. 3777 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2671 (Rfree = 0.000) for 2892 atoms. Found 20 (20 requested) and removed 34 (12 requested) atoms. Cycle 12: After refmac, R = 0.2413 (Rfree = 0.000) for 2868 atoms. Found 12 (19 requested) and removed 14 (12 requested) atoms. Cycle 13: After refmac, R = 0.2315 (Rfree = 0.000) for 2861 atoms. Found 6 (19 requested) and removed 12 (12 requested) atoms. Cycle 14: After refmac, R = 0.2284 (Rfree = 0.000) for 2853 atoms. Found 3 (18 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.2246 (Rfree = 0.000) for 2842 atoms. Found 2 (18 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward Round 1: 276 peptides, 32 chains. Longest chain 35 peptides. Score 0.680 Round 2: 265 peptides, 28 chains. Longest chain 51 peptides. Score 0.697 Round 3: 280 peptides, 28 chains. Longest chain 51 peptides. Score 0.728 Round 4: 283 peptides, 27 chains. Longest chain 37 peptides. Score 0.743 Round 5: 291 peptides, 26 chains. Longest chain 41 peptides. Score 0.767 Taking the results from Round 5 Chains 30, Residues 265, Estimated correctness of the model 78.1 % 4 chains (85 residues) have been docked in sequence Building loops using Loopy2018 30 chains (265 residues) following loop building 4 chains (85 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5285 restraints for refining 2891 atoms. 3905 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2582 (Rfree = 0.000) for 2891 atoms. Found 17 (17 requested) and removed 27 (12 requested) atoms. Cycle 17: After refmac, R = 0.2308 (Rfree = 0.000) for 2879 atoms. Found 14 (17 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 2876 atoms. Found 8 (16 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2154 (Rfree = 0.000) for 2867 atoms. Found 2 (16 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2094 (Rfree = 0.000) for 2857 atoms. Found 4 (15 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward Round 1: 267 peptides, 29 chains. Longest chain 38 peptides. Score 0.691 Round 2: 282 peptides, 28 chains. Longest chain 43 peptides. Score 0.732 Round 3: 287 peptides, 29 chains. Longest chain 43 peptides. Score 0.733 Round 4: 290 peptides, 27 chains. Longest chain 43 peptides. Score 0.756 Round 5: 287 peptides, 26 chains. Longest chain 43 peptides. Score 0.760 Taking the results from Round 5 Chains 27, Residues 261, Estimated correctness of the model 76.9 % 3 chains (80 residues) have been docked in sequence Building loops using Loopy2018 27 chains (261 residues) following loop building 3 chains (80 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5414 restraints for refining 2892 atoms. 4070 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2433 (Rfree = 0.000) for 2892 atoms. Found 15 (15 requested) and removed 25 (12 requested) atoms. Cycle 22: After refmac, R = 0.2118 (Rfree = 0.000) for 2877 atoms. Found 7 (14 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.1999 (Rfree = 0.000) for 2864 atoms. Found 8 (14 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1987 (Rfree = 0.000) for 2856 atoms. Found 5 (13 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1882 (Rfree = 0.000) for 2846 atoms. Found 3 (13 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.10 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward Round 1: 257 peptides, 32 chains. Longest chain 42 peptides. Score 0.634 Round 2: 263 peptides, 25 chains. Longest chain 23 peptides. Score 0.723 Round 3: 275 peptides, 34 chains. Longest chain 32 peptides. Score 0.656 Round 4: 276 peptides, 28 chains. Longest chain 21 peptides. Score 0.720 Round 5: 269 peptides, 30 chains. Longest chain 42 peptides. Score 0.685 Taking the results from Round 2 Chains 26, Residues 238, Estimated correctness of the model 69.9 % 3 chains (37 residues) have been docked in sequence Building loops using Loopy2018 26 chains (238 residues) following loop building 3 chains (37 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 6060 restraints for refining 2892 atoms. 5009 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2082 (Rfree = 0.000) for 2892 atoms. Found 12 (12 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.1933 (Rfree = 0.000) for 2887 atoms. Found 3 (12 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.1978 (Rfree = 0.000) for 2876 atoms. Found 5 (12 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.1802 (Rfree = 0.000) for 2866 atoms. Found 3 (12 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1743 (Rfree = 0.000) for 2853 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.11 Search for helices and strands: 0 residues in 0 chains, 2933 seeds are put forward Round 1: 257 peptides, 32 chains. Longest chain 31 peptides. Score 0.634 Round 2: 275 peptides, 25 chains. Longest chain 32 peptides. Score 0.746 Round 3: 266 peptides, 24 chains. Longest chain 32 peptides. Score 0.738 Round 4: 271 peptides, 27 chains. Longest chain 30 peptides. Score 0.720 Round 5: 269 peptides, 27 chains. Longest chain 22 peptides. Score 0.716 Taking the results from Round 2 Chains 26, Residues 250, Estimated correctness of the model 74.3 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 26 chains (250 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5676 restraints for refining 2892 atoms. 4485 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2021 (Rfree = 0.000) for 2892 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 32: After refmac, R = 0.1916 (Rfree = 0.000) for 2882 atoms. Found 7 (12 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.1759 (Rfree = 0.000) for 2875 atoms. Found 8 (12 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 2870 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1725 (Rfree = 0.000) for 2857 atoms. Found 3 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward Round 1: 262 peptides, 35 chains. Longest chain 16 peptides. Score 0.611 Round 2: 270 peptides, 27 chains. Longest chain 31 peptides. Score 0.718 Round 3: 287 peptides, 30 chains. Longest chain 32 peptides. Score 0.724 Round 4: 287 peptides, 29 chains. Longest chain 32 peptides. Score 0.733 Round 5: 284 peptides, 32 chains. Longest chain 28 peptides. Score 0.698 Taking the results from Round 4 Chains 30, Residues 258, Estimated correctness of the model 71.9 % 3 chains (35 residues) have been docked in sequence Building loops using Loopy2018 30 chains (258 residues) following loop building 3 chains (35 residues) in sequence following loop building ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 5905 restraints for refining 2891 atoms. 4756 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2055 (Rfree = 0.000) for 2891 atoms. Found 12 (12 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.1915 (Rfree = 0.000) for 2882 atoms. Found 10 (12 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1776 (Rfree = 0.000) for 2877 atoms. Found 5 (12 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.1834 (Rfree = 0.000) for 2869 atoms. Found 6 (12 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1706 (Rfree = 0.000) for 2862 atoms. Found 5 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward Round 1: 223 peptides, 27 chains. Longest chain 31 peptides. Score 0.603 Round 2: 225 peptides, 24 chains. Longest chain 33 peptides. Score 0.645 Round 3: 227 peptides, 24 chains. Longest chain 22 peptides. Score 0.651 Round 4: 220 peptides, 24 chains. Longest chain 23 peptides. Score 0.632 Round 5: 227 peptides, 26 chains. Longest chain 21 peptides. Score 0.626 Taking the results from Round 3 Chains 26, Residues 203, Estimated correctness of the model 54.1 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7062 reflections ( 99.80 % complete ) and 6266 restraints for refining 2891 atoms. 5358 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1960 (Rfree = 0.000) for 2891 atoms. Found 12 (12 requested) and removed 21 (12 requested) atoms. Cycle 42: After refmac, R = 0.1857 (Rfree = 0.000) for 2878 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.1702 (Rfree = 0.000) for 2878 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1686 (Rfree = 0.000) for 2869 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1637 (Rfree = 0.000) for 2867 atoms. Found 9 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 2947 seeds are put forward Round 1: 219 peptides, 28 chains. Longest chain 18 peptides. Score 0.578 Round 2: 251 peptides, 27 chains. Longest chain 29 peptides. Score 0.675 Round 3: 246 peptides, 28 chains. Longest chain 22 peptides. Score 0.652 Round 4: 249 peptides, 30 chains. Longest chain 32 peptides. Score 0.636 Round 5: 250 peptides, 25 chains. Longest chain 31 peptides. Score 0.695 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 225, Estimated correctness of the model 64.1 % 3 chains (39 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2ozg-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (225 residues) following loop building 3 chains (39 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7062 reflections ( 99.80 % complete ) and 6064 restraints for refining 2892 atoms. 5078 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2020 (Rfree = 0.000) for 2892 atoms. Found 0 (12 requested) and removed 7 (12 requested) atoms. Cycle 47: After refmac, R = 0.2067 (Rfree = 0.000) for 2882 atoms. Found 0 (12 requested) and removed 3 (12 requested) atoms. Cycle 48: After refmac, R = 0.1887 (Rfree = 0.000) for 2876 atoms. Found 0 (12 requested) and removed 3 (12 requested) atoms. Cycle 49: After refmac, R = 0.1826 (Rfree = 0.000) for 2873 atoms. Found 0 (12 requested) and removed 0 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:23:00 GMT 2018 Job finished. TimeTaking 60.23 Used memory is bytes: 6865952