Mon 24 Dec 07:37:14 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 2hq7-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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/2hq7-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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 07:37:18 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/2hq7-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.5089 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-2.0-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.50 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 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: 89.671 2.000 Wilson plot Bfac: 25.26 19227 reflections ( 99.63 % complete ) and 0 restraints for refining 2585 atoms. Observations/parameters ratio is 1.86 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2691 (Rfree = 0.000) for 2585 atoms. Found 66 (88 requested) and removed 52 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 2.31 NCS extension: 0 residues added, 2599 seeds are put forward Round 1: 183 peptides, 22 chains. Longest chain 34 peptides. Score 0.665 Round 2: 229 peptides, 14 chains. Longest chain 46 peptides. Score 0.870 Round 3: 239 peptides, 8 chains. Longest chain 57 peptides. Score 0.923 Round 4: 246 peptides, 11 chains. Longest chain 57 peptides. Score 0.911 Round 5: 241 peptides, 11 chains. Longest chain 57 peptides. Score 0.906 Taking the results from Round 3 Chains 8, Residues 231, Estimated correctness of the model 99.4 % 6 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 B and 81 B Built loop between residues 114 B and 117 B 5 chains (238 residues) following loop building 4 chains (223 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2679 restraints for refining 2352 atoms. 795 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3109 (Rfree = 0.000) for 2352 atoms. Found 69 (80 requested) and removed 43 (40 requested) atoms. Cycle 2: After refmac, R = 0.2817 (Rfree = 0.000) for 2370 atoms. Found 56 (79 requested) and removed 40 (40 requested) atoms. Cycle 3: After refmac, R = 0.2662 (Rfree = 0.000) for 2371 atoms. Found 47 (78 requested) and removed 36 (40 requested) atoms. Cycle 4: After refmac, R = 0.2542 (Rfree = 0.000) for 2375 atoms. Found 49 (76 requested) and removed 23 (40 requested) atoms. Cycle 5: After refmac, R = 0.2452 (Rfree = 0.000) for 2393 atoms. Found 30 (77 requested) and removed 13 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.10 2.28 NCS extension: 19 residues added (34 deleted due to clashes), 2437 seeds are put forward Round 1: 244 peptides, 9 chains. Longest chain 54 peptides. Score 0.921 Round 2: 246 peptides, 7 chains. Longest chain 67 peptides. Score 0.934 Round 3: 252 peptides, 10 chains. Longest chain 44 peptides. Score 0.923 Round 4: 248 peptides, 8 chains. Longest chain 76 peptides. Score 0.930 Round 5: 256 peptides, 6 chains. Longest chain 88 peptides. Score 0.946 Taking the results from Round 5 Chains 6, Residues 250, Estimated correctness of the model 99.7 % 6 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 73 A and 78 A Built loop between residues 100 A and 105 A Built loop between residues 52 B and 55 B 2 chains (262 residues) following loop building 2 chains (262 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2445 restraints for refining 2451 atoms. 272 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2569 (Rfree = 0.000) for 2451 atoms. Found 51 (78 requested) and removed 44 (41 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 2450 atoms. Found 38 (77 requested) and removed 42 (42 requested) atoms. Cycle 8: After refmac, R = 0.2286 (Rfree = 0.000) for 2443 atoms. Found 37 (75 requested) and removed 40 (41 requested) atoms. Cycle 9: After refmac, R = 0.2217 (Rfree = 0.000) for 2435 atoms. Found 36 (73 requested) and removed 28 (41 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 2439 atoms. Found 43 (71 requested) and removed 33 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2452 seeds are put forward Round 1: 258 peptides, 5 chains. Longest chain 133 peptides. Score 0.952 Round 2: 259 peptides, 5 chains. Longest chain 77 peptides. Score 0.953 Round 3: 257 peptides, 8 chains. Longest chain 85 peptides. Score 0.937 Round 4: 261 peptides, 7 chains. Longest chain 67 peptides. Score 0.945 Round 5: 265 peptides, 4 chains. Longest chain 124 peptides. Score 0.960 Taking the results from Round 5 Chains 4, Residues 261, Estimated correctness of the model 99.8 % 3 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 95 A 3 chains (263 residues) following loop building 2 chains (256 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2435 restraints for refining 2433 atoms. 278 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2367 (Rfree = 0.000) for 2433 atoms. Found 58 (70 requested) and removed 41 (41 requested) atoms. Cycle 12: After refmac, R = 0.2202 (Rfree = 0.000) for 2444 atoms. Found 41 (68 requested) and removed 41 (41 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 2442 atoms. Found 42 (66 requested) and removed 27 (41 requested) atoms. Cycle 14: After refmac, R = 0.2031 (Rfree = 0.000) for 2453 atoms. Found 42 (66 requested) and removed 12 (42 requested) atoms. Cycle 15: After refmac, R = 0.1970 (Rfree = 0.000) for 2481 atoms. Found 32 (66 requested) and removed 20 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.08 2.25 NCS extension: 5 residues added (6 deleted due to clashes), 2500 seeds are put forward Round 1: 267 peptides, 3 chains. Longest chain 134 peptides. Score 0.966 Round 2: 266 peptides, 4 chains. Longest chain 134 peptides. Score 0.961 Round 3: 264 peptides, 6 chains. Longest chain 72 peptides. Score 0.951 Round 4: 266 peptides, 4 chains. Longest chain 134 peptides. Score 0.961 Round 5: 265 peptides, 6 chains. Longest chain 85 peptides. Score 0.952 Taking the results from Round 1 Chains 3, Residues 264, Estimated correctness of the model 99.9 % 3 chains (264 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 B and 104 B 2 chains (266 residues) following loop building 2 chains (266 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2422 restraints for refining 2476 atoms. 215 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2235 (Rfree = 0.000) for 2476 atoms. Found 64 (64 requested) and removed 45 (42 requested) atoms. Cycle 17: After refmac, R = 0.2113 (Rfree = 0.000) for 2490 atoms. Found 55 (63 requested) and removed 42 (42 requested) atoms. Cycle 18: After refmac, R = 0.2032 (Rfree = 0.000) for 2499 atoms. Found 43 (61 requested) and removed 35 (42 requested) atoms. Cycle 19: After refmac, R = 0.1993 (Rfree = 0.000) for 2502 atoms. Found 42 (59 requested) and removed 36 (42 requested) atoms. Cycle 20: After refmac, R = 0.1964 (Rfree = 0.000) for 2505 atoms. Found 43 (58 requested) and removed 30 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2518 seeds are put forward Round 1: 264 peptides, 4 chains. Longest chain 134 peptides. Score 0.960 Round 2: 260 peptides, 4 chains. Longest chain 131 peptides. Score 0.958 Round 3: 260 peptides, 6 chains. Longest chain 85 peptides. Score 0.949 Round 4: 262 peptides, 4 chains. Longest chain 134 peptides. Score 0.959 Round 5: 265 peptides, 5 chains. Longest chain 85 peptides. Score 0.956 Taking the results from Round 1 Chains 5, Residues 260, Estimated correctness of the model 99.8 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 B and 80 B 4 chains (262 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2560 restraints for refining 2472 atoms. 449 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2208 (Rfree = 0.000) for 2472 atoms. Found 55 (55 requested) and removed 44 (42 requested) atoms. Cycle 22: After refmac, R = 0.2078 (Rfree = 0.000) for 2479 atoms. Found 49 (54 requested) and removed 22 (42 requested) atoms. Cycle 23: After refmac, R = 0.2008 (Rfree = 0.000) for 2504 atoms. Found 40 (54 requested) and removed 33 (42 requested) atoms. Cycle 24: After refmac, R = 0.1963 (Rfree = 0.000) for 2511 atoms. Found 45 (53 requested) and removed 29 (42 requested) atoms. Cycle 25: After refmac, R = 0.1922 (Rfree = 0.000) for 2524 atoms. Found 41 (52 requested) and removed 35 (43 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.08 2.25 NCS extension: 2 residues added (11 deleted due to clashes), 2532 seeds are put forward Round 1: 260 peptides, 6 chains. Longest chain 134 peptides. Score 0.949 Round 2: 264 peptides, 4 chains. Longest chain 123 peptides. Score 0.960 Round 3: 263 peptides, 7 chains. Longest chain 77 peptides. Score 0.946 Round 4: 267 peptides, 4 chains. Longest chain 123 peptides. Score 0.961 Round 5: 265 peptides, 6 chains. Longest chain 75 peptides. Score 0.952 Taking the results from Round 4 Chains 4, Residues 263, Estimated correctness of the model 99.8 % 3 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 80 A 3 chains (267 residues) following loop building 2 chains (258 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2502 restraints for refining 2487 atoms. 317 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2213 (Rfree = 0.000) for 2487 atoms. Found 49 (49 requested) and removed 43 (42 requested) atoms. Cycle 27: After refmac, R = 0.2054 (Rfree = 0.000) for 2492 atoms. Found 44 (48 requested) and removed 27 (42 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 2506 atoms. Found 37 (46 requested) and removed 35 (42 requested) atoms. Cycle 29: After refmac, R = 0.1928 (Rfree = 0.000) for 2508 atoms. Found 44 (44 requested) and removed 28 (42 requested) atoms. Cycle 30: After refmac, R = 0.1914 (Rfree = 0.000) for 2522 atoms. Found 43 (43 requested) and removed 32 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.08 2.25 NCS extension: 7 residues added (6 deleted due to clashes), 2540 seeds are put forward Round 1: 265 peptides, 5 chains. Longest chain 134 peptides. Score 0.956 Round 2: 265 peptides, 5 chains. Longest chain 122 peptides. Score 0.956 Round 3: 263 peptides, 7 chains. Longest chain 76 peptides. Score 0.946 Round 4: 265 peptides, 6 chains. Longest chain 74 peptides. Score 0.952 Round 5: 265 peptides, 6 chains. Longest chain 76 peptides. Score 0.952 Taking the results from Round 2 Chains 6, Residues 260, Estimated correctness of the model 99.8 % 4 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 78 A Built loop between residues 100 A and 104 A 4 chains (265 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2501 restraints for refining 2462 atoms. 350 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2179 (Rfree = 0.000) for 2462 atoms. Found 42 (42 requested) and removed 42 (42 requested) atoms. Cycle 32: After refmac, R = 0.2039 (Rfree = 0.000) for 2462 atoms. Found 42 (42 requested) and removed 23 (42 requested) atoms. Cycle 33: After refmac, R = 0.1972 (Rfree = 0.000) for 2480 atoms. Found 42 (42 requested) and removed 28 (42 requested) atoms. Cycle 34: After refmac, R = 0.1942 (Rfree = 0.000) for 2494 atoms. Found 42 (42 requested) and removed 34 (42 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 2502 atoms. Found 42 (42 requested) and removed 28 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.08 2.25 NCS extension: 56 residues added (102 deleted due to clashes), 2575 seeds are put forward Round 1: 262 peptides, 6 chains. Longest chain 122 peptides. Score 0.950 Round 2: 262 peptides, 6 chains. Longest chain 125 peptides. Score 0.950 Round 3: 264 peptides, 6 chains. Longest chain 134 peptides. Score 0.951 Round 4: 264 peptides, 8 chains. Longest chain 70 peptides. Score 0.942 Round 5: 258 peptides, 9 chains. Longest chain 122 peptides. Score 0.933 Taking the results from Round 3 Chains 6, Residues 258, Estimated correctness of the model 99.7 % 4 chains (243 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 B and 104 B 5 chains (261 residues) following loop building 3 chains (246 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2664 restraints for refining 2467 atoms. 561 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2189 (Rfree = 0.000) for 2467 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2048 (Rfree = 0.000) for 2465 atoms. Found 42 (42 requested) and removed 29 (42 requested) atoms. Cycle 38: After refmac, R = 0.1973 (Rfree = 0.000) for 2478 atoms. Found 42 (42 requested) and removed 25 (42 requested) atoms. Cycle 39: After refmac, R = 0.1928 (Rfree = 0.000) for 2494 atoms. Found 42 (42 requested) and removed 26 (42 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 2509 atoms. Found 36 (42 requested) and removed 27 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.08 2.25 NCS extension: 57 residues added (98 deleted due to clashes), 2576 seeds are put forward Round 1: 261 peptides, 6 chains. Longest chain 83 peptides. Score 0.949 Round 2: 264 peptides, 5 chains. Longest chain 133 peptides. Score 0.956 Round 3: 264 peptides, 6 chains. Longest chain 76 peptides. Score 0.951 Round 4: 264 peptides, 6 chains. Longest chain 84 peptides. Score 0.951 Round 5: 264 peptides, 7 chains. Longest chain 56 peptides. Score 0.947 Taking the results from Round 2 Chains 5, Residues 259, Estimated correctness of the model 99.8 % 3 chains (245 residues) have been docked in sequence Building loops using Loopy2018 5 chains (259 residues) following loop building 3 chains (245 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2614 restraints for refining 2470 atoms. 523 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2123 (Rfree = 0.000) for 2470 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 42: After refmac, R = 0.2002 (Rfree = 0.000) for 2467 atoms. Found 42 (42 requested) and removed 23 (42 requested) atoms. Cycle 43: After refmac, R = 0.1948 (Rfree = 0.000) for 2484 atoms. Found 31 (42 requested) and removed 33 (42 requested) atoms. Cycle 44: After refmac, R = 0.1897 (Rfree = 0.000) for 2482 atoms. Found 42 (42 requested) and removed 21 (42 requested) atoms. Cycle 45: After refmac, R = 0.1861 (Rfree = 0.000) for 2503 atoms. Found 42 (42 requested) and removed 28 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.08 2.25 NCS extension: 56 residues added (98 deleted due to clashes), 2573 seeds are put forward Round 1: 258 peptides, 7 chains. Longest chain 83 peptides. Score 0.943 Round 2: 263 peptides, 6 chains. Longest chain 93 peptides. Score 0.951 Round 3: 263 peptides, 8 chains. Longest chain 66 peptides. Score 0.941 Round 4: 265 peptides, 6 chains. Longest chain 84 peptides. Score 0.952 Round 5: 260 peptides, 8 chains. Longest chain 56 peptides. Score 0.939 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 259, Estimated correctness of the model 99.7 % 5 chains (250 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 74 A and 78 A Built loop between residues 91 A and 94 A Built loop between residues 92 B and 95 B 3 chains (266 residues) following loop building 2 chains (257 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19227 reflections ( 99.63 % complete ) and 2165 restraints for refining 2121 atoms. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2650 (Rfree = 0.000) for 2121 atoms. Found 16 (36 requested) and removed 0 (36 requested) atoms. Cycle 47: After refmac, R = 0.2499 (Rfree = 0.000) for 2121 atoms. Found 10 (36 requested) and removed 0 (36 requested) atoms. Cycle 48: After refmac, R = 0.2388 (Rfree = 0.000) for 2121 atoms. Found 7 (36 requested) and removed 0 (36 requested) atoms. Cycle 49: After refmac, R = 0.2318 (Rfree = 0.000) for 2121 atoms. TimeTaking 34.35