Sun 23 Dec 22:23:02 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 2gno-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-2.0-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/2gno-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-2.0-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 22:23:12 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/2gno-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-2.0-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 275 and 0 Target number of residues in the AU: 275 Target solvent content: 0.5445 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-2.0-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 target number of atoms Had to go as low as 0.55 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 1 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: 95.855 2.000 Wilson plot Bfac: 33.82 22236 reflections ( 99.69 % complete ) and 0 restraints for refining 2710 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Starting model: R = 0.3439 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 2710 atoms. Found 23 (92 requested) and removed 56 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.39 Round 1: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.438 Round 2: 200 peptides, 26 chains. Longest chain 18 peptides. Score 0.619 Round 3: 213 peptides, 20 chains. Longest chain 22 peptides. Score 0.740 Round 4: 223 peptides, 20 chains. Longest chain 40 peptides. Score 0.764 Round 5: 236 peptides, 17 chains. Longest chain 40 peptides. Score 0.820 Taking the results from Round 5 Chains 17, Residues 219, Estimated correctness of the model 96.9 % 3 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 220 A and 223 A 16 chains (221 residues) following loop building 2 chains (111 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 3589 restraints for refining 2366 atoms. 2247 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3292 (Rfree = 0.000) for 2366 atoms. Found 36 (81 requested) and removed 44 (40 requested) atoms. Cycle 2: After refmac, R = 0.3037 (Rfree = 0.000) for 2333 atoms. Found 37 (78 requested) and removed 40 (40 requested) atoms. Cycle 3: After refmac, R = 0.2882 (Rfree = 0.000) for 2321 atoms. Found 24 (76 requested) and removed 16 (39 requested) atoms. Cycle 4: After refmac, R = 0.2772 (Rfree = 0.000) for 2326 atoms. Found 16 (74 requested) and removed 8 (39 requested) atoms. Cycle 5: After refmac, R = 0.2739 (Rfree = 0.000) for 2331 atoms. Found 10 (74 requested) and removed 5 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.25 2.28 Round 1: 233 peptides, 17 chains. Longest chain 39 peptides. Score 0.815 Round 2: 236 peptides, 16 chains. Longest chain 41 peptides. Score 0.829 Round 3: 240 peptides, 14 chains. Longest chain 41 peptides. Score 0.852 Round 4: 240 peptides, 18 chains. Longest chain 36 peptides. Score 0.818 Round 5: 221 peptides, 16 chains. Longest chain 37 peptides. Score 0.802 Taking the results from Round 3 Chains 14, Residues 226, Estimated correctness of the model 97.9 % 5 chains (154 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 220 A and 223 A 13 chains (228 residues) following loop building 4 chains (156 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 3263 restraints for refining 2366 atoms. 1690 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2907 (Rfree = 0.000) for 2366 atoms. Found 34 (76 requested) and removed 43 (40 requested) atoms. Cycle 7: After refmac, R = 0.2720 (Rfree = 0.000) for 2355 atoms. Found 17 (74 requested) and removed 5 (40 requested) atoms. Cycle 8: After refmac, R = 0.2651 (Rfree = 0.000) for 2360 atoms. Found 14 (75 requested) and removed 8 (40 requested) atoms. Cycle 9: After refmac, R = 0.2607 (Rfree = 0.000) for 2362 atoms. Found 13 (73 requested) and removed 7 (40 requested) atoms. Cycle 10: After refmac, R = 0.2574 (Rfree = 0.000) for 2365 atoms. Found 10 (71 requested) and removed 4 (40 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.26 2.29 Round 1: 241 peptides, 15 chains. Longest chain 55 peptides. Score 0.846 Round 2: 256 peptides, 13 chains. Longest chain 56 peptides. Score 0.881 Round 3: 249 peptides, 15 chains. Longest chain 41 peptides. Score 0.857 Round 4: 251 peptides, 12 chains. Longest chain 88 peptides. Score 0.882 Round 5: 252 peptides, 16 chains. Longest chain 58 peptides. Score 0.854 Taking the results from Round 4 Chains 13, Residues 239, Estimated correctness of the model 98.6 % 6 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 45 A Built loop between residues 180 A and 187 A 11 chains (251 residues) following loop building 4 chains (211 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2889 restraints for refining 2479 atoms. 991 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2880 (Rfree = 0.000) for 2479 atoms. Found 37 (74 requested) and removed 46 (42 requested) atoms. Cycle 12: After refmac, R = 0.2684 (Rfree = 0.000) for 2465 atoms. Found 49 (72 requested) and removed 42 (42 requested) atoms. Cycle 13: After refmac, R = 0.2564 (Rfree = 0.000) for 2468 atoms. Found 37 (71 requested) and removed 17 (42 requested) atoms. Cycle 14: After refmac, R = 0.2503 (Rfree = 0.000) for 2480 atoms. Found 39 (71 requested) and removed 20 (42 requested) atoms. Cycle 15: After refmac, R = 0.2446 (Rfree = 0.000) for 2498 atoms. Found 24 (70 requested) and removed 8 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.25 2.28 Round 1: 256 peptides, 14 chains. Longest chain 74 peptides. Score 0.874 Round 2: 262 peptides, 12 chains. Longest chain 52 peptides. Score 0.894 Round 3: 259 peptides, 14 chains. Longest chain 56 peptides. Score 0.878 Round 4: 256 peptides, 18 chains. Longest chain 39 peptides. Score 0.844 Round 5: 267 peptides, 11 chains. Longest chain 94 peptides. Score 0.905 Taking the results from Round 5 Chains 12, Residues 256, Estimated correctness of the model 99.0 % 6 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 180 A and 183 A Built loop between residues 200 A and 203 A 9 chains (262 residues) following loop building 3 chains (209 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2898 restraints for refining 2521 atoms. 961 conditional restraints added. Observations/parameters ratio is 2.21 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2852 (Rfree = 0.000) for 2521 atoms. Found 52 (71 requested) and removed 44 (43 requested) atoms. Cycle 17: After refmac, R = 0.2610 (Rfree = 0.000) for 2524 atoms. Found 32 (69 requested) and removed 29 (43 requested) atoms. Cycle 18: After refmac, R = 0.2505 (Rfree = 0.000) for 2521 atoms. Found 24 (67 requested) and removed 25 (43 requested) atoms. Cycle 19: After refmac, R = 0.2437 (Rfree = 0.000) for 2513 atoms. Found 20 (65 requested) and removed 14 (43 requested) atoms. Cycle 20: After refmac, R = 0.2392 (Rfree = 0.000) for 2515 atoms. Found 23 (64 requested) and removed 14 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.25 2.28 Round 1: 263 peptides, 12 chains. Longest chain 78 peptides. Score 0.895 Round 2: 271 peptides, 10 chains. Longest chain 116 peptides. Score 0.915 Round 3: 272 peptides, 12 chains. Longest chain 81 peptides. Score 0.904 Round 4: 264 peptides, 12 chains. Longest chain 114 peptides. Score 0.896 Round 5: 272 peptides, 11 chains. Longest chain 69 peptides. Score 0.910 Taking the results from Round 2 Chains 11, Residues 261, Estimated correctness of the model 99.2 % 5 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 58 A and 63 A Built loop between residues 180 A and 183 A 8 chains (269 residues) following loop building 2 chains (241 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2788 restraints for refining 2558 atoms. 689 conditional restraints added. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2700 (Rfree = 0.000) for 2558 atoms. Found 50 (63 requested) and removed 45 (43 requested) atoms. Cycle 22: After refmac, R = 0.2535 (Rfree = 0.000) for 2561 atoms. Found 45 (61 requested) and removed 33 (43 requested) atoms. Cycle 23: After refmac, R = 0.2447 (Rfree = 0.000) for 2567 atoms. Found 27 (60 requested) and removed 12 (44 requested) atoms. Cycle 24: After refmac, R = 0.2396 (Rfree = 0.000) for 2576 atoms. Found 22 (60 requested) and removed 15 (44 requested) atoms. Cycle 25: After refmac, R = 0.2345 (Rfree = 0.000) for 2580 atoms. Found 23 (58 requested) and removed 16 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.25 2.28 Round 1: 259 peptides, 10 chains. Longest chain 49 peptides. Score 0.904 Round 2: 265 peptides, 8 chains. Longest chain 116 peptides. Score 0.920 Round 3: 268 peptides, 9 chains. Longest chain 73 peptides. Score 0.917 Round 4: 262 peptides, 10 chains. Longest chain 63 peptides. Score 0.906 Round 5: 259 peptides, 9 chains. Longest chain 72 peptides. Score 0.909 Taking the results from Round 2 Chains 8, Residues 257, Estimated correctness of the model 99.3 % 3 chains (230 residues) have been docked in sequence Building loops using Loopy2018 8 chains (257 residues) following loop building 3 chains (230 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2973 restraints for refining 2603 atoms. 948 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 2603 atoms. Found 44 (57 requested) and removed 48 (44 requested) atoms. Cycle 27: After refmac, R = 0.2510 (Rfree = 0.000) for 2598 atoms. Found 24 (55 requested) and removed 27 (44 requested) atoms. Cycle 28: After refmac, R = 0.2420 (Rfree = 0.000) for 2592 atoms. Found 29 (53 requested) and removed 14 (44 requested) atoms. Cycle 29: After refmac, R = 0.2385 (Rfree = 0.000) for 2603 atoms. Found 24 (53 requested) and removed 16 (44 requested) atoms. Cycle 30: After refmac, R = 0.2322 (Rfree = 0.000) for 2603 atoms. Found 25 (52 requested) and removed 6 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.25 2.28 Round 1: 267 peptides, 10 chains. Longest chain 73 peptides. Score 0.911 Round 2: 265 peptides, 7 chains. Longest chain 95 peptides. Score 0.926 Round 3: 270 peptides, 8 chains. Longest chain 116 peptides. Score 0.924 Round 4: 270 peptides, 8 chains. Longest chain 76 peptides. Score 0.924 Round 5: 266 peptides, 9 chains. Longest chain 70 peptides. Score 0.916 Taking the results from Round 2 Chains 8, Residues 258, Estimated correctness of the model 99.4 % 4 chains (229 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 183 A Built loop between residues 221 A and 232 A 4 chains (266 residues) following loop building 2 chains (246 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2867 restraints for refining 2624 atoms. 765 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2675 (Rfree = 0.000) for 2624 atoms. Found 44 (52 requested) and removed 48 (44 requested) atoms. Cycle 32: After refmac, R = 0.2497 (Rfree = 0.000) for 2618 atoms. Found 27 (50 requested) and removed 23 (44 requested) atoms. Cycle 33: After refmac, R = 0.2404 (Rfree = 0.000) for 2613 atoms. Found 15 (48 requested) and removed 14 (44 requested) atoms. Cycle 34: After refmac, R = 0.2368 (Rfree = 0.000) for 2609 atoms. Found 15 (46 requested) and removed 7 (44 requested) atoms. Cycle 35: After refmac, R = 0.2342 (Rfree = 0.000) for 2614 atoms. Failed to save intermediate PDB Found 8 (46 requested) and removed 7 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.25 2.28 Round 1: 265 peptides, 6 chains. Longest chain 113 peptides. Score 0.931 Round 2: 259 peptides, 7 chains. Longest chain 78 peptides. Score 0.921 Round 3: 265 peptides, 9 chains. Longest chain 88 peptides. Score 0.915 Round 4: 275 peptides, 7 chains. Longest chain 116 peptides. Score 0.933 Round 5: 265 peptides, 5 chains. Longest chain 114 peptides. Score 0.936 Taking the results from Round 5 Chains 5, Residues 260, Estimated correctness of the model 99.5 % 3 chains (244 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 182 A 4 chains (263 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2882 restraints for refining 2596 atoms. 793 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2588 (Rfree = 0.000) for 2596 atoms. Found 39 (44 requested) and removed 46 (44 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 2587 atoms. Found 25 (44 requested) and removed 16 (44 requested) atoms. Cycle 38: After refmac, R = 0.2350 (Rfree = 0.000) for 2594 atoms. Found 21 (44 requested) and removed 6 (44 requested) atoms. Cycle 39: After refmac, R = 0.2312 (Rfree = 0.000) for 2608 atoms. Found 21 (44 requested) and removed 8 (44 requested) atoms. Cycle 40: After refmac, R = 0.2279 (Rfree = 0.000) for 2618 atoms. Found 16 (44 requested) and removed 8 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.25 2.28 Round 1: 264 peptides, 10 chains. Longest chain 73 peptides. Score 0.908 Round 2: 270 peptides, 6 chains. Longest chain 147 peptides. Score 0.935 Round 3: 262 peptides, 10 chains. Longest chain 68 peptides. Score 0.906 Round 4: 272 peptides, 8 chains. Longest chain 88 peptides. Score 0.926 Round 5: 270 peptides, 7 chains. Longest chain 92 peptides. Score 0.930 Taking the results from Round 2 Chains 6, Residues 264, Estimated correctness of the model 99.5 % 3 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A 5 chains (266 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ 22236 reflections ( 99.69 % complete ) and 2822 restraints for refining 2618 atoms. 717 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2503 (Rfree = 0.000) for 2618 atoms. Found 35 (44 requested) and removed 48 (44 requested) atoms. Cycle 42: After refmac, R = 0.2364 (Rfree = 0.000) for 2602 atoms. Found 24 (44 requested) and removed 20 (44 requested) atoms. Cycle 43: After refmac, R = 0.2296 (Rfree = 0.000) for 2606 atoms. Found 13 (44 requested) and removed 9 (44 requested) atoms. Cycle 44: After refmac, R = 0.2260 (Rfree = 0.000) for 2610 atoms. Found 14 (44 requested) and removed 8 (44 requested) atoms. Cycle 45: After refmac, R = 0.2229 (Rfree = 0.000) for 2616 atoms. Found 19 (44 requested) and removed 7 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.28 Round 1: 262 peptides, 9 chains. Longest chain 72 peptides. Score 0.912 Round 2: 261 peptides, 11 chains. Longest chain 79 peptides. Score 0.899 Round 3: 268 peptides, 10 chains. Longest chain 84 peptides. Score 0.912 Round 4: 266 peptides, 9 chains. Longest chain 95 peptides. Score 0.916 Round 5: 270 peptides, 7 chains. Longest chain 93 peptides. Score 0.930 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 263, Estimated correctness of the model 99.5 % 3 chains (214 residues) have been docked in sequence Sequence coverage is 81 % All DUM atoms will be removed Building loops using Loopy2018 7 chains (263 residues) following loop building 3 chains (214 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22236 reflections ( 99.69 % complete ) and 1970 restraints for refining 1951 atoms. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3626 (Rfree = 0.000) for 1951 atoms. Found 9 (33 requested) and removed 0 (33 requested) atoms. Cycle 47: After refmac, R = 0.3485 (Rfree = 0.000) for 1951 atoms. Found 5 (33 requested) and removed 0 (33 requested) atoms. Cycle 48: After refmac, R = 0.3408 (Rfree = 0.000) for 1951 atoms. Found 2 (33 requested) and removed 1 (33 requested) atoms. Cycle 49: After refmac, R = 0.3362 (Rfree = 0.000) for 1951 atoms. TimeTaking 55.63