null Mon 24 Dec 07:56:35 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 2prx-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prx-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prx-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 07:56:40 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/noncs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 296 and 0 Target number of residues in the AU: 296 Target solvent content: 0.4551 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2560 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: 28.816 2.000 Wilson plot Bfac: 15.36 19184 reflections ( 99.72 % complete ) and 0 restraints for refining 2863 atoms. Observations/parameters ratio is 1.68 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2997 (Rfree = 0.000) for 2863 atoms. Found 70 (98 requested) and removed 57 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 2.17 NCS extension: 0 residues added, 2876 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 9 peptides. Score 0.265 Round 2: 116 peptides, 24 chains. Longest chain 8 peptides. Score 0.292 Round 3: 116 peptides, 23 chains. Longest chain 12 peptides. Score 0.317 Round 4: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.419 Round 5: 130 peptides, 21 chains. Longest chain 22 peptides. Score 0.442 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 75.6 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5101 restraints for refining 2483 atoms. 4672 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3090 (Rfree = 0.000) for 2483 atoms. Found 83 (85 requested) and removed 44 (42 requested) atoms. Cycle 2: After refmac, R = 0.2790 (Rfree = 0.000) for 2522 atoms. Found 63 (86 requested) and removed 31 (43 requested) atoms. Cycle 3: After refmac, R = 0.2578 (Rfree = 0.000) for 2554 atoms. Found 45 (87 requested) and removed 14 (43 requested) atoms. Cycle 4: After refmac, R = 0.2417 (Rfree = 0.000) for 2585 atoms. Found 40 (88 requested) and removed 2 (44 requested) atoms. Cycle 5: After refmac, R = 0.2324 (Rfree = 0.000) for 2622 atoms. Found 26 (89 requested) and removed 5 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.82 2.05 NCS extension: 0 residues added, 2665 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 12 peptides. Score 0.322 Round 2: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.355 Round 3: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.405 Round 4: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.419 Round 5: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 4 Chains 19, Residues 98, Estimated correctness of the model 73.8 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5528 restraints for refining 2582 atoms. 5138 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2541 (Rfree = 0.000) for 2582 atoms. Found 66 (88 requested) and removed 29 (44 requested) atoms. Cycle 7: After refmac, R = 0.2344 (Rfree = 0.000) for 2619 atoms. Found 47 (89 requested) and removed 6 (44 requested) atoms. Cycle 8: After refmac, R = 0.2220 (Rfree = 0.000) for 2660 atoms. Found 45 (91 requested) and removed 4 (45 requested) atoms. Cycle 9: After refmac, R = 0.2155 (Rfree = 0.000) for 2700 atoms. Found 40 (92 requested) and removed 1 (46 requested) atoms. Cycle 10: After refmac, R = 0.2114 (Rfree = 0.000) for 2737 atoms. Found 33 (93 requested) and removed 5 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.82 2.05 NCS extension: 0 residues added, 2775 seeds are put forward Round 1: 143 peptides, 30 chains. Longest chain 8 peptides. Score 0.305 Round 2: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.383 Round 3: 139 peptides, 25 chains. Longest chain 10 peptides. Score 0.399 Round 4: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.372 Round 5: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 5 Chains 24, Residues 113, Estimated correctness of the model 74.5 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5465 restraints for refining 2685 atoms. 4974 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2455 (Rfree = 0.000) for 2685 atoms. Found 91 (91 requested) and removed 38 (45 requested) atoms. Cycle 12: After refmac, R = 0.2254 (Rfree = 0.000) for 2737 atoms. Found 58 (93 requested) and removed 7 (46 requested) atoms. Cycle 13: After refmac, R = 0.2117 (Rfree = 0.000) for 2786 atoms. Found 57 (95 requested) and removed 8 (47 requested) atoms. Cycle 14: After refmac, R = 0.2055 (Rfree = 0.000) for 2832 atoms. Found 45 (97 requested) and removed 4 (48 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 2872 atoms. Found 46 (98 requested) and removed 8 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.80 2.03 NCS extension: 0 residues added, 2927 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.320 Round 2: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.471 Round 3: 154 peptides, 25 chains. Longest chain 11 peptides. Score 0.476 Round 4: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.479 Round 5: 143 peptides, 23 chains. Longest chain 13 peptides. Score 0.464 Taking the results from Round 4 Chains 23, Residues 123, Estimated correctness of the model 78.5 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5667 restraints for refining 2798 atoms. 5153 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 2798 atoms. Found 95 (95 requested) and removed 42 (47 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 2850 atoms. Found 66 (97 requested) and removed 6 (48 requested) atoms. Cycle 18: After refmac, R = 0.1976 (Rfree = 0.000) for 2910 atoms. Found 38 (99 requested) and removed 7 (49 requested) atoms. Cycle 19: After refmac, R = 0.1927 (Rfree = 0.000) for 2938 atoms. Found 44 (100 requested) and removed 5 (50 requested) atoms. Cycle 20: After refmac, R = 0.1890 (Rfree = 0.000) for 2974 atoms. Found 33 (101 requested) and removed 7 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.79 2.02 NCS extension: 0 residues added, 3020 seeds are put forward Round 1: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.359 Round 2: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.421 Round 3: 122 peptides, 20 chains. Longest chain 12 peptides. Score 0.423 Round 4: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.434 Round 5: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Chains 21, Residues 104, Estimated correctness of the model 75.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6263 restraints for refining 2919 atoms. 5836 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2147 (Rfree = 0.000) for 2919 atoms. Found 100 (100 requested) and removed 41 (50 requested) atoms. Cycle 22: After refmac, R = 0.2014 (Rfree = 0.000) for 2977 atoms. Found 59 (102 requested) and removed 16 (51 requested) atoms. Cycle 23: After refmac, R = 0.1893 (Rfree = 0.000) for 3020 atoms. Found 51 (103 requested) and removed 6 (51 requested) atoms. Cycle 24: After refmac, R = 0.1849 (Rfree = 0.000) for 3065 atoms. Found 32 (105 requested) and removed 7 (52 requested) atoms. Cycle 25: After refmac, R = 0.1810 (Rfree = 0.000) for 3089 atoms. Found 35 (105 requested) and removed 14 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.79 2.02 NCS extension: 0 residues added, 3120 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 12 peptides. Score 0.377 Round 2: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.383 Round 3: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.399 Round 4: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.405 Round 5: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 4 Chains 21, Residues 102, Estimated correctness of the model 72.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6489 restraints for refining 2963 atoms. 6102 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2047 (Rfree = 0.000) for 2963 atoms. Found 101 (101 requested) and removed 14 (50 requested) atoms. Cycle 27: After refmac, R = 0.1944 (Rfree = 0.000) for 3050 atoms. Found 58 (104 requested) and removed 12 (52 requested) atoms. Cycle 28: After refmac, R = 0.1867 (Rfree = 0.000) for 3094 atoms. Found 61 (106 requested) and removed 13 (53 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 3140 atoms. Found 70 (107 requested) and removed 20 (53 requested) atoms. Cycle 30: After refmac, R = 0.1785 (Rfree = 0.000) for 3187 atoms. Found 60 (109 requested) and removed 27 (54 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 2.02 NCS extension: 4 residues added (0 deleted due to clashes), 3232 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.302 Round 2: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.385 Round 3: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.423 Round 4: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.362 Round 5: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 5 Chains 20, Residues 102, Estimated correctness of the model 74.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6667 restraints for refining 3053 atoms. 6279 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2035 (Rfree = 0.000) for 3053 atoms. Found 104 (104 requested) and removed 32 (52 requested) atoms. Cycle 32: After refmac, R = 0.1855 (Rfree = 0.000) for 3125 atoms. Found 76 (107 requested) and removed 6 (53 requested) atoms. Cycle 33: After refmac, R = 0.1779 (Rfree = 0.000) for 3195 atoms. Found 58 (109 requested) and removed 13 (54 requested) atoms. Cycle 34: After refmac, R = 0.1743 (Rfree = 0.000) for 3238 atoms. Found 59 (110 requested) and removed 24 (55 requested) atoms. Cycle 35: After refmac, R = 0.1702 (Rfree = 0.000) for 3271 atoms. Found 55 (112 requested) and removed 29 (56 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.78 2.01 NCS extension: 0 residues added, 3304 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.294 Round 2: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.377 Round 3: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.366 Round 4: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.385 Round 5: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 71.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6830 restraints for refining 3097 atoms. 6503 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1927 (Rfree = 0.000) for 3097 atoms. Found 106 (106 requested) and removed 22 (53 requested) atoms. Cycle 37: After refmac, R = 0.1816 (Rfree = 0.000) for 3181 atoms. Found 97 (108 requested) and removed 9 (54 requested) atoms. Cycle 38: After refmac, R = 0.1749 (Rfree = 0.000) for 3269 atoms. Found 55 (111 requested) and removed 40 (55 requested) atoms. Cycle 39: After refmac, R = 0.1692 (Rfree = 0.000) for 3284 atoms. Found 69 (112 requested) and removed 20 (56 requested) atoms. Cycle 40: After refmac, R = 0.1661 (Rfree = 0.000) for 3332 atoms. Found 51 (114 requested) and removed 43 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 2.02 NCS extension: 0 residues added, 3347 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 10 peptides. Score 0.298 Round 2: 104 peptides, 19 chains. Longest chain 10 peptides. Score 0.346 Round 3: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.321 Round 4: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Round 5: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.362 Taking the results from Round 4 Chains 19, Residues 90, Estimated correctness of the model 70.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 7051 restraints for refining 3125 atoms. 6710 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1951 (Rfree = 0.000) for 3125 atoms. Found 107 (107 requested) and removed 16 (53 requested) atoms. Cycle 42: After refmac, R = 0.1802 (Rfree = 0.000) for 3216 atoms. Found 98 (110 requested) and removed 12 (55 requested) atoms. Cycle 43: After refmac, R = 0.1710 (Rfree = 0.000) for 3301 atoms. Found 74 (113 requested) and removed 31 (56 requested) atoms. Cycle 44: After refmac, R = 0.1676 (Rfree = 0.000) for 3344 atoms. Found 69 (114 requested) and removed 39 (57 requested) atoms. Cycle 45: After refmac, R = 0.1633 (Rfree = 0.000) for 3374 atoms. Found 85 (115 requested) and removed 41 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.78 2.01 NCS extension: 6 residues added (0 deleted due to clashes), 3432 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.280 Round 2: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.383 Round 3: 101 peptides, 18 chains. Longest chain 12 peptides. Score 0.354 Round 4: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.316 Round 5: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 88, Estimated correctness of the model 70.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prx-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19184 reflections ( 99.72 % complete ) and 7259 restraints for refining 3182 atoms. 6925 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1846 (Rfree = 0.000) for 3182 atoms. Found 0 (109 requested) and removed 2 (54 requested) atoms. Cycle 47: After refmac, R = 0.1793 (Rfree = 0.000) for 3180 atoms. Found 0 (108 requested) and removed 0 (54 requested) atoms. Cycle 48: After refmac, R = 0.1763 (Rfree = 0.000) for 3180 atoms. Found 0 (108 requested) and removed 1 (54 requested) atoms. Cycle 49: After refmac, R = 0.1769 (Rfree = 0.000) for 3179 atoms. Found 0 (108 requested) and removed 0 (54 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:29:07 GMT 2018 Job finished. TimeTaking 32.54 Used memory is bytes: 5784280