null Mon 24 Dec 07:55:55 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 2p8j-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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/2p8j-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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 07:55:59 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/2p8j-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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 398 and 0 Target number of residues in the AU: 398 Target solvent content: 0.6668 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-4.0-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: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.10 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: 72.625 4.000 Wilson plot Bfac: 89.83 5718 reflections ( 98.03 % complete ) and 0 restraints for refining 3727 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3237 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.10 Search for helices and strands: 0 residues in 0 chains, 3798 seeds are put forward NCS extension: 0 residues added, 3798 seeds are put forward Round 1: 197 peptides, 36 chains. Longest chain 11 peptides. Score 0.328 Round 2: 241 peptides, 32 chains. Longest chain 15 peptides. Score 0.484 Round 3: 253 peptides, 33 chains. Longest chain 17 peptides. Score 0.501 Round 4: 261 peptides, 30 chains. Longest chain 20 peptides. Score 0.548 Round 5: 264 peptides, 34 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 4 Chains 30, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6712 restraints for refining 3020 atoms. 5818 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2850 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2828 (Rfree = 0.000) for 2997 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2843 (Rfree = 0.000) for 2980 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.2854 (Rfree = 0.000) for 2971 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2804 (Rfree = 0.000) for 2964 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.11 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3073 seeds are put forward Round 1: 227 peptides, 33 chains. Longest chain 16 peptides. Score 0.440 Round 2: 255 peptides, 28 chains. Longest chain 20 peptides. Score 0.555 Round 3: 258 peptides, 30 chains. Longest chain 21 peptides. Score 0.542 Round 4: 268 peptides, 33 chains. Longest chain 22 peptides. Score 0.534 Round 5: 265 peptides, 30 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 5 Chains 30, Residues 235, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6567 restraints for refining 3018 atoms. 5581 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2597 (Rfree = 0.000) for 3018 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2411 (Rfree = 0.000) for 2986 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 2974 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. Cycle 9: After refmac, R = 0.2349 (Rfree = 0.000) for 2960 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.2302 (Rfree = 0.000) for 2952 atoms. Found 0 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.09 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3062 seeds are put forward Round 1: 225 peptides, 33 chains. Longest chain 19 peptides. Score 0.436 Round 2: 242 peptides, 33 chains. Longest chain 20 peptides. Score 0.476 Round 3: 256 peptides, 31 chains. Longest chain 22 peptides. Score 0.528 Round 4: 266 peptides, 33 chains. Longest chain 23 peptides. Score 0.530 Round 5: 277 peptides, 34 chains. Longest chain 22 peptides. Score 0.543 Taking the results from Round 5 Chains 34, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6674 restraints for refining 3020 atoms. 5736 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2812 (Rfree = 0.000) for 3020 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2741 (Rfree = 0.000) for 2997 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 13: After refmac, R = 0.2699 (Rfree = 0.000) for 2988 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2585 (Rfree = 0.000) for 2983 atoms. Found 11 (14 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2592 (Rfree = 0.000) for 2974 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.12 Search for helices and strands: 0 residues in 0 chains, 3091 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3111 seeds are put forward Round 1: 209 peptides, 31 chains. Longest chain 14 peptides. Score 0.418 Round 2: 238 peptides, 27 chains. Longest chain 21 peptides. Score 0.529 Round 3: 249 peptides, 28 chains. Longest chain 20 peptides. Score 0.543 Round 4: 245 peptides, 27 chains. Longest chain 24 peptides. Score 0.544 Round 5: 265 peptides, 32 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 4 Chains 27, Residues 218, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6631 restraints for refining 3020 atoms. 5676 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2654 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.2387 (Rfree = 0.000) for 2990 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 18: After refmac, R = 0.2334 (Rfree = 0.000) for 2963 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2201 (Rfree = 0.000) for 2953 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 20: After refmac, R = 0.2255 (Rfree = 0.000) for 2942 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.13 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3069 seeds are put forward Round 1: 227 peptides, 36 chains. Longest chain 14 peptides. Score 0.407 Round 2: 237 peptides, 31 chains. Longest chain 20 peptides. Score 0.486 Round 3: 244 peptides, 31 chains. Longest chain 26 peptides. Score 0.502 Round 4: 248 peptides, 27 chains. Longest chain 20 peptides. Score 0.551 Round 5: 248 peptides, 28 chains. Longest chain 27 peptides. Score 0.541 Taking the results from Round 4 Chains 27, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6866 restraints for refining 3020 atoms. 6009 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2741 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.2552 (Rfree = 0.000) for 3003 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.2358 (Rfree = 0.000) for 3003 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.2281 (Rfree = 0.000) for 2991 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 25: After refmac, R = 0.2040 (Rfree = 0.000) for 2985 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.12 Search for helices and strands: 0 residues in 0 chains, 3103 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3128 seeds are put forward Round 1: 198 peptides, 31 chains. Longest chain 14 peptides. Score 0.390 Round 2: 238 peptides, 30 chains. Longest chain 28 peptides. Score 0.498 Round 3: 249 peptides, 25 chains. Longest chain 42 peptides. Score 0.572 Round 4: 250 peptides, 28 chains. Longest chain 41 peptides. Score 0.545 Round 5: 232 peptides, 31 chains. Longest chain 18 peptides. Score 0.474 Taking the results from Round 3 Chains 27, Residues 224, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6309 restraints for refining 3020 atoms. 5276 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2472 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2336 (Rfree = 0.000) for 2983 atoms. Found 7 (14 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.2263 (Rfree = 0.000) for 2960 atoms. Found 2 (14 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.2220 (Rfree = 0.000) for 2941 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.2190 (Rfree = 0.000) for 2922 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3020 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3052 seeds are put forward Round 1: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.376 Round 2: 239 peptides, 33 chains. Longest chain 23 peptides. Score 0.469 Round 3: 244 peptides, 32 chains. Longest chain 16 peptides. Score 0.491 Round 4: 241 peptides, 30 chains. Longest chain 30 peptides. Score 0.505 Round 5: 232 peptides, 29 chains. Longest chain 23 peptides. Score 0.495 Taking the results from Round 4 Chains 30, Residues 211, Estimated correctness of the model 0.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6425 restraints for refining 3019 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2662 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 32: After refmac, R = 0.2554 (Rfree = 0.000) for 2987 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.2645 (Rfree = 0.000) for 2975 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.2217 (Rfree = 0.000) for 2964 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.2162 (Rfree = 0.000) for 2954 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.11 Search for helices and strands: 0 residues in 0 chains, 3042 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3063 seeds are put forward Round 1: 210 peptides, 36 chains. Longest chain 19 peptides. Score 0.363 Round 2: 231 peptides, 34 chains. Longest chain 17 peptides. Score 0.439 Round 3: 225 peptides, 29 chains. Longest chain 18 peptides. Score 0.479 Round 4: 219 peptides, 29 chains. Longest chain 19 peptides. Score 0.465 Round 5: 229 peptides, 29 chains. Longest chain 21 peptides. Score 0.488 Taking the results from Round 5 Chains 30, Residues 200, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6758 restraints for refining 3019 atoms. 5943 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2849 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 37: After refmac, R = 0.2598 (Rfree = 0.000) for 2983 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 38: After refmac, R = 0.2210 (Rfree = 0.000) for 2959 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 39: After refmac, R = 0.2405 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 40: After refmac, R = 0.2597 (Rfree = 0.000) for 2937 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 3036 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3051 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 18 peptides. Score 0.329 Round 2: 206 peptides, 30 chains. Longest chain 19 peptides. Score 0.422 Round 3: 210 peptides, 29 chains. Longest chain 20 peptides. Score 0.443 Round 4: 201 peptides, 31 chains. Longest chain 19 peptides. Score 0.398 Round 5: 212 peptides, 30 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 3 Chains 29, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6947 restraints for refining 3020 atoms. 6252 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2772 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 42: After refmac, R = 0.2579 (Rfree = 0.000) for 2992 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.2639 (Rfree = 0.000) for 2976 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 44: After refmac, R = 0.2481 (Rfree = 0.000) for 2960 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 45: After refmac, R = 0.2610 (Rfree = 0.000) for 2955 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3108 seeds are put forward Round 1: 170 peptides, 30 chains. Longest chain 13 peptides. Score 0.326 Round 2: 189 peptides, 27 chains. Longest chain 19 peptides. Score 0.414 Round 3: 200 peptides, 29 chains. Longest chain 16 peptides. Score 0.418 Round 4: 216 peptides, 28 chains. Longest chain 26 peptides. Score 0.469 Round 5: 217 peptides, 29 chains. Longest chain 25 peptides. Score 0.460 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 188, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2p8j-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5718 reflections ( 98.03 % complete ) and 6712 restraints for refining 3020 atoms. 5935 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2568 (Rfree = 0.000) for 3020 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2557 (Rfree = 0.000) for 2992 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2520 (Rfree = 0.000) for 2974 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2386 (Rfree = 0.000) for 2953 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:33:47 GMT 2018 Job finished. TimeTaking 37.87 Used memory is bytes: 16522928