Sun 23 Dec 23:48:36 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 2o08-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-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/2o08-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-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 ============================================================ Sun 23 Dec 23:48:40 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/2o08-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-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 352 and 0 Target number of residues in the AU: 352 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.8-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3008 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: 83.235 3.800 Wilson plot Bfac: 78.33 5512 reflections ( 97.49 % complete ) and 0 restraints for refining 3311 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3375 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2976 (Rfree = 0.000) for 3311 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.11 Search for helices and strands: 0 residues in 0 chains, 3429 seeds are put forward NCS extension: 0 residues added, 3429 seeds are put forward Round 1: 197 peptides, 32 chains. Longest chain 11 peptides. Score 0.402 Round 2: 219 peptides, 28 chains. Longest chain 17 peptides. Score 0.514 Round 3: 221 peptides, 27 chains. Longest chain 20 peptides. Score 0.531 Round 4: 212 peptides, 22 chains. Longest chain 20 peptides. Score 0.567 Round 5: 209 peptides, 25 chains. Longest chain 18 peptides. Score 0.524 Taking the results from Round 4 Chains 24, Residues 190, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5995 restraints for refining 2721 atoms. 5220 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2807 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 2: After refmac, R = 0.2695 (Rfree = 0.000) for 2680 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2380 (Rfree = 0.000) for 2662 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2368 (Rfree = 0.000) for 2640 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2240 (Rfree = 0.000) for 2630 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2797 seeds are put forward Round 1: 201 peptides, 33 chains. Longest chain 14 peptides. Score 0.401 Round 2: 227 peptides, 26 chains. Longest chain 18 peptides. Score 0.557 Round 3: 221 peptides, 29 chains. Longest chain 15 peptides. Score 0.507 Round 4: 208 peptides, 23 chains. Longest chain 20 peptides. Score 0.545 Round 5: 219 peptides, 28 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 2 Chains 26, Residues 201, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5919 restraints for refining 2721 atoms. 5105 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2524 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.2328 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 2692 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2092 (Rfree = 0.000) for 2689 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2030 (Rfree = 0.000) for 2682 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2833 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2851 seeds are put forward Round 1: 197 peptides, 30 chains. Longest chain 14 peptides. Score 0.428 Round 2: 223 peptides, 29 chains. Longest chain 22 peptides. Score 0.512 Round 3: 228 peptides, 27 chains. Longest chain 14 peptides. Score 0.548 Round 4: 225 peptides, 23 chains. Longest chain 21 peptides. Score 0.586 Round 5: 225 peptides, 23 chains. Longest chain 23 peptides. Score 0.586 Taking the results from Round 5 Chains 23, Residues 202, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5914 restraints for refining 2721 atoms. 5105 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2546 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2489 (Rfree = 0.000) for 2700 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.2178 (Rfree = 0.000) for 2691 atoms. Found 7 (14 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.2296 (Rfree = 0.000) for 2672 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 15: After refmac, R = 0.2186 (Rfree = 0.000) for 2658 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 2844 seeds are put forward Round 1: 206 peptides, 34 chains. Longest chain 15 peptides. Score 0.403 Round 2: 206 peptides, 25 chains. Longest chain 19 peptides. Score 0.516 Round 3: 209 peptides, 27 chains. Longest chain 19 peptides. Score 0.500 Round 4: 212 peptides, 27 chains. Longest chain 15 peptides. Score 0.508 Round 5: 226 peptides, 26 chains. Longest chain 21 peptides. Score 0.555 Taking the results from Round 5 Chains 26, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6002 restraints for refining 2720 atoms. 5228 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2675 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 2691 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 18: After refmac, R = 0.2267 (Rfree = 0.000) for 2677 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 19: After refmac, R = 0.2254 (Rfree = 0.000) for 2662 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 20: After refmac, R = 0.2223 (Rfree = 0.000) for 2634 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 2.94 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 2809 seeds are put forward Round 1: 220 peptides, 38 chains. Longest chain 14 peptides. Score 0.393 Round 2: 227 peptides, 32 chains. Longest chain 15 peptides. Score 0.487 Round 3: 208 peptides, 24 chains. Longest chain 16 peptides. Score 0.533 Round 4: 231 peptides, 30 chains. Longest chain 18 peptides. Score 0.521 Round 5: 221 peptides, 26 chains. Longest chain 18 peptides. Score 0.542 Taking the results from Round 5 Chains 27, Residues 195, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5851 restraints for refining 2721 atoms. 5034 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 22: After refmac, R = 0.2188 (Rfree = 0.000) for 2692 atoms. Found 13 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2121 (Rfree = 0.000) for 2682 atoms. Found 6 (14 requested) and removed 23 (7 requested) atoms. Cycle 24: After refmac, R = 0.2124 (Rfree = 0.000) for 2659 atoms. Found 10 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.2024 (Rfree = 0.000) for 2654 atoms. Found 7 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 2.95 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2798 seeds are put forward Round 1: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.349 Round 2: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.423 Round 3: 213 peptides, 30 chains. Longest chain 17 peptides. Score 0.474 Round 4: 231 peptides, 34 chains. Longest chain 14 peptides. Score 0.474 Round 5: 218 peptides, 32 chains. Longest chain 18 peptides. Score 0.463 Taking the results from Round 4 Chains 35, Residues 197, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5823 restraints for refining 2720 atoms. 5039 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2401 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 2700 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.2132 (Rfree = 0.000) for 2695 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.2132 (Rfree = 0.000) for 2687 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2156 (Rfree = 0.000) for 2685 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.98 Search for helices and strands: 0 residues in 0 chains, 2840 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2853 seeds are put forward Round 1: 188 peptides, 35 chains. Longest chain 13 peptides. Score 0.334 Round 2: 200 peptides, 32 chains. Longest chain 15 peptides. Score 0.411 Round 3: 195 peptides, 30 chains. Longest chain 18 peptides. Score 0.422 Round 4: 193 peptides, 27 chains. Longest chain 15 peptides. Score 0.456 Round 5: 197 peptides, 22 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 5 Chains 23, Residues 175, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5981 restraints for refining 2721 atoms. 5261 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2477 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 40 (7 requested) atoms. Cycle 32: After refmac, R = 0.2304 (Rfree = 0.000) for 2687 atoms. Found 11 (14 requested) and removed 19 (7 requested) atoms. Cycle 33: After refmac, R = 0.2444 (Rfree = 0.000) for 2673 atoms. Found 5 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.2271 (Rfree = 0.000) for 2654 atoms. Found 5 (14 requested) and removed 15 (7 requested) atoms. Cycle 35: After refmac, R = 0.2479 (Rfree = 0.000) for 2640 atoms. Found 5 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 2734 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2764 seeds are put forward Round 1: 165 peptides, 30 chains. Longest chain 12 peptides. Score 0.329 Round 2: 183 peptides, 31 chains. Longest chain 14 peptides. Score 0.373 Round 3: 184 peptides, 29 chains. Longest chain 15 peptides. Score 0.403 Round 4: 187 peptides, 31 chains. Longest chain 20 peptides. Score 0.385 Round 5: 195 peptides, 29 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 5 Chains 29, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6188 restraints for refining 2721 atoms. 5553 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2314 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 37: After refmac, R = 0.2169 (Rfree = 0.000) for 2702 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.2085 (Rfree = 0.000) for 2695 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.2061 (Rfree = 0.000) for 2684 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2041 (Rfree = 0.000) for 2675 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2817 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 9 peptides. Score 0.261 Round 2: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.331 Round 3: 173 peptides, 29 chains. Longest chain 13 peptides. Score 0.369 Round 4: 182 peptides, 28 chains. Longest chain 15 peptides. Score 0.410 Round 5: 187 peptides, 28 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 28, Residues 159, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6206 restraints for refining 2720 atoms. 5562 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2443 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.2252 (Rfree = 0.000) for 2713 atoms. Found 4 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.2247 (Rfree = 0.000) for 2700 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2274 (Rfree = 0.000) for 2695 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.2331 (Rfree = 0.000) for 2684 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.04 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2831 seeds are put forward Round 1: 144 peptides, 30 chains. Longest chain 10 peptides. Score 0.257 Round 2: 161 peptides, 26 chains. Longest chain 14 peptides. Score 0.373 Round 3: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.401 Round 4: 156 peptides, 25 chains. Longest chain 12 peptides. Score 0.371 Round 5: 149 peptides, 26 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 151, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5512 reflections ( 97.49 % complete ) and 6253 restraints for refining 2721 atoms. 5677 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2683 (Rfree = 0.000) for 2721 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2383 (Rfree = 0.000) for 2694 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2355 (Rfree = 0.000) for 2675 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2408 (Rfree = 0.000) for 2655 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. TimeTaking 32.9